ISDA

Deposition Date 2016-11-09

Release Date 2017-01-18

Last Version Date 2025-07-09

Entry Detail

PDB ID:

5MC6

Keywords:

RIBOSOME

Title:

Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae

Biological Source:

Source Organism:

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.80 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:A (auth: 2)
Chain Length:1800
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:B (auth: A)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05750 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:PA (auth: AA)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P17076 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:QA (auth: AB)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX41 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:RA (auth: AC)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05745 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:SA (auth: AD)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05738 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:TA (auth: AE)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P04449 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:UA (auth: AF)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P49166 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-A
Gene (Uniprot):RPL11A
Chain IDs:VA (auth: AG)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:WA (auth: AH)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P04456 Pfam ID:PF03939, PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:XA (auth: AI)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P49167 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:YA (auth: AJ)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q12690 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:ZA (auth: AK)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05743 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:AB (auth: AL)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P04650 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:BB (auth: AM)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P36105 Pfam ID:PF00467, PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:CB (auth: AN)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C2H6 Pfam ID:PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):RPL40A
Chain IDs:DB (auth: AO)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CH08 Pfam ID:PF00240, PF01020

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:EB (auth: AP)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX27 Pfam ID:PF00935

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:FB (auth: AQ)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05748 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:GB (auth: AR)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P02406 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-A
Gene (Uniprot):RPL41A
Chain IDs:HB (auth: AS)
Chain Length:25
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX86 Pfam ID:PF05162

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:IB (auth: AT)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX25 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:JB (auth: AU)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P26784 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:KB (auth: AV)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05747 Pfam ID:PF01779

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:LB (auth: AW)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX45 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:MB (auth: AX)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05740 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:NB (auth: AY)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P14120 Pfam ID:PF01248

Polymer Type:polypeptide(L)
Molecule:uL1
Chain IDs:OB (auth: AZ)
Chain Length:210
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:C (auth: B)
Chain Length:225
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P26783 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:PB (auth: BA)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P14126 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:QB (auth: BB)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX49 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:RB (auth: BC)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C2H8 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:SB (auth: BD)
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P41805 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:TB (auth: BE)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P10664 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:UB (auth: BF)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX82 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:VB (auth: BG)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38061 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:WB (auth: BH)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX23 Pfam ID:PF01775

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:XB (auth: BI)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P26321 Pfam ID:PF17144, PF14204

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:YB (auth: BJ)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q02753 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:ZB (auth: BK)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05744 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:AC (auth: BL)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05749 Pfam ID:PF01776

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:BC (auth: BM)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q02326 Pfam ID:PF01159

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:CC (auth: BN)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P87262 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:DC (auth: BO)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05737 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:EC (auth: BP)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX84 Pfam ID:PF00831

Polymer Type:polyribonucleotide
Molecule:25S ribosomal RNA
Chain IDs:FC (auth: BQ)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:GC (auth: BR)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:HC (auth: BS)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 5A-1
Gene (Uniprot):HYP2
Chain IDs:IC (auth: BT)
Chain Length:157
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P23301 Pfam ID:PF21485, PF01287

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A
Gene (Uniprot):RPS10A
Chain IDs:D (auth: C)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q08745 Pfam ID:PF03501

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:E (auth: D)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P48589 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:F (auth: E)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q01855 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:G (auth: F)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX51 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17-B
Gene (Uniprot):RPS17B
Chain IDs:H (auth: G)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P14127 Pfam ID:PF00833

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-A
Gene (Uniprot):RPS18A
Chain IDs:I (auth: H)
Chain Length:1287
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX55 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19-A
Gene (Uniprot):RPS19A
Chain IDs:J (auth: I)
Chain Length:1432
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P07280 Pfam ID:PF01090

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:K (auth: J)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38701 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25-A
Gene (Uniprot):RPS25A
Chain IDs:L (auth: K)
Chain Length:397
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q3E792 Pfam ID:PF03297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-B
Gene (Uniprot):RPS28B
Chain IDs:M (auth: L)
Chain Length:34
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C0X0 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29-A
Gene (Uniprot):RPS29A
Chain IDs:N (auth: M)
Chain Length:56
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P41057 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31
Gene (Uniprot):RPS31
Chain IDs:O (auth: N)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05759 Pfam ID:PF00240, PF01599

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-like protein
Gene (Uniprot):ASC1
Chain IDs:P (auth: O)
Chain Length:319
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38011 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0-A
Gene (Uniprot):RPS0A
Chain IDs:Q (auth: P)
Chain Length:252
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P32905 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1-A
Gene (Uniprot):RPS1A
Chain IDs:R (auth: Q)
Chain Length:255
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P33442 Pfam ID:PF01015

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:S (auth: R)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P25443 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:T (auth: S)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX35 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:U (auth: T)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX37 Pfam ID:PF01092

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:V (auth: U)
Chain Length:190
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P26786 Pfam ID:PF01251

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:W (auth: V)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX39 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:X (auth: W)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:O13516 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:Y (auth: X)
Chain Length:156
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX47 Pfam ID:PF16205, PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:Z (auth: Y)
Chain Length:151
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05756 Pfam ID:PF08069, PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Gene (Uniprot):RPS14A
Chain IDs:AA (auth: Z)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P06367 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21-A
Gene (Uniprot):RPS21A
Chain IDs:BA (auth: a)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C0V8 Pfam ID:PF01249

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Gene (Uniprot):RPS22A
Chain IDs:CA (auth: b)
Chain Length:225
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C0W1 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:DA (auth: c)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX29 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:EA (auth: d)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX31 Pfam ID:PF01282

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26-A
Gene (Uniprot):RPS26A
Chain IDs:FA (auth: e)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P39938 Pfam ID:PF01283

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:GA (auth: f)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P35997 Pfam ID:PF01667

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30-A
Gene (Uniprot):RPS30A
Chain IDs:HA (auth: g)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX33 Pfam ID:PF04758

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Antiviral helicase SKI2
Gene (Uniprot):SKI2
Chain IDs:LA (auth: h)
Chain Length:1287
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P35207 Pfam ID:PF17911, PF00270, PF00271, PF21408, PF21409, PF08148

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Superkiller protein 3
Gene (Uniprot):SKI3
Chain IDs:MA (auth: i)
Chain Length:1432
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P17883 Pfam ID:PF18833

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Antiviral protein SKI8
Gene (Uniprot):SKI8
Chain IDs:NA (auth: j), OA (auth: k)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q02793 Pfam ID:PF00400

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:IA (auth: l)
Chain Length:34
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Polymer Type:polyribonucleotide
Molecule:A-site tRNA
Chain IDs:JA (auth: m)
Chain Length:56
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:KA (auth: n)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
5CT	IC	LYS	modified residue

Ligand Molecules

Primary Citation

The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex.

Schmidt, C, Kowalinski, E, Shanmuganathan, V, Defenouillere, Q, Braunger, K, Heuer, A, Pech, M, Namane, A, Berninghausen, O, Fromont-Racine, M, Jacquier, A, Conti, E, Becker, T, Beckmann, R.Show

Science 354 1431 1433 (2016)

PMID: 27980209 DOI: 10.1126/science.aaf7520

Abstact

Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski complex directly associates with 80S ribosomes presenting a short mRNA 3' overhang. We determined the structure of an endogenous ribosome-Ski complex using cryo-electron microscopy (EM) with a local resolution of the Ski complex ranging from 4 angstroms (Å) in the core to about 10 Å for intrinsically flexible regions. Ribosome binding displaces the autoinhibitory domain of the Ski2 helicase, positioning it in an open conformation near the ribosomal mRNA entry tunnel. We observe that the mRNA 3' overhang is threaded directly from the small ribosomal subunit to the helicase channel of Ski2, primed for ongoing exosome-mediated 3'-5' degradation.

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Primary Citation of related structures