ISDA

Deposition Date 2018-12-16

Release Date 2019-03-13

Last Version Date 2025-07-02

Entry Detail

PDB ID:

6Q8Y

Keywords:

TRANSLATION

Title:

Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex

Biological Source:

Source Organism:

Saccharomyces cerevisiae (Taxon ID: 4932)

Host Organism:

Saccharomyces cerevisiae

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.10 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:1797
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:EB (auth: A)
Chain Length:223
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05750 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:B (auth: AA)
Chain Length:233
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P17076 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:C (auth: AB)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX41 Pfam ID:PF00238

Protein Blast

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

UniProt ID:P05745 Pfam ID:PF01158

Protein Blast

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

UniProt ID:P05738 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:F (auth: AE)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P04449 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:G (auth: AF)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P49166 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-B
Gene (Uniprot):RPL11B
Chain IDs:H (auth: AG)
Chain Length:169
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q3E757 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:I (auth: AH)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P04456 Pfam ID:PF03939, PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:J (auth: AI)
Chain Length:77
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P49167 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:K (auth: AJ)
Chain Length:193
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q12690 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:L (auth: AK)
Chain Length:126
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05743 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:M (auth: AL)
Chain Length:50
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P04650 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:N (auth: AM)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P36105 Pfam ID:PF00467, PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:O (auth: AN)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0C2H6 Pfam ID:PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):RPL40A
Chain IDs:P (auth: AO)
Chain Length:52
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CH08 Pfam ID:PF01020

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:Q (auth: AP)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX27 Pfam ID:PF00935

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:R (auth: AQ)
Chain Length:203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05748 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:S (auth: AR)
Chain Length:148
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P02406 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-B
Gene (Uniprot):RPL41B
Chain IDs:T (auth: AS)
Chain Length:25
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX87 Pfam ID:PF05162

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:U (auth: AT)
Chain Length:91
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX25 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:V (auth: AU)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P26784 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:W (auth: AV)
Chain Length:58
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05747 Pfam ID:PF01779

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:X (auth: AW)
Chain Length:252
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX45 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:Y (auth: AX)
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05740 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:KA (auth: AY)
Chain Length:97
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P14120 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Rps5p
Gene (Uniprot):RPS5
Chain IDs:FB (auth: B)
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:A0A1L4AA68 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:LA (auth: BA)
Chain Length:386
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P14126 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:MA (auth: BB)
Chain Length:185
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX49 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:NA (auth: BC)
Chain Length:109
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0C2H8 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:OA (auth: BD)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P41805 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:PA (auth: BE)
Chain Length:361
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P10664 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:QA (auth: BF)
Chain Length:188
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX82 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:RA (auth: BG)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38061 Pfam ID:PF01655

Protein Blast

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

UniProt ID:P0CX23 Pfam ID:PF01775

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:TA (auth: BI)
Chain Length:296
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P26321 Pfam ID:PF17144, PF14204

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:UA (auth: BJ)
Chain Length:159
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q02753 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:VA (auth: BK)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05744 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:WA (auth: BL)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05749 Pfam ID:PF01776

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:XA (auth: BM)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q02326 Pfam ID:PF01159

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:YA (auth: BN)
Chain Length:112
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P87262 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:ZA (auth: BO)
Chain Length:222
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05737 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:AB (auth: BP)
Chain Length:119
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX84 Pfam ID:PF00831

Polymer Type:polyribonucleotide
Molecule:25S ribosomal RNA
Chain IDs:BB (auth: BQ)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:CB (auth: BR)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:DB (auth: BS)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A
Gene (Uniprot):RPS10A
Chain IDs:GB (auth: C)
Chain Length:144
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q08745 Pfam ID:PF03501

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:HB (auth: D)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P48589 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:IB (auth: E)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q01855 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:JB (auth: F)
Chain Length:141
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX51 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17-A
Gene (Uniprot):RPS17A
Chain IDs:KB (auth: G)
Chain Length:60
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P02407 Pfam ID:PF00833

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-A
Gene (Uniprot):RPS18A
Chain IDs:LB (auth: H)
Chain Length:139
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX55 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19-A
Gene (Uniprot):RPS19A
Chain IDs:DC (auth: I)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P07280 Pfam ID:PF01090

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:MB (auth: J)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38701 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25-A
Gene (Uniprot):RPS25A
Chain IDs:NB (auth: K)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q3E792 Pfam ID:PF03297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-A
Gene (Uniprot):RPS28A
Chain IDs:OB (auth: L)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q3E7X9 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29-A
Gene (Uniprot):RPS29A
Chain IDs:PB (auth: M)
Chain Length:53
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P41057 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31
Gene (Uniprot):RPS31
Chain IDs:QB (auth: N)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05759 Pfam ID:PF01599

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-like protein
Gene (Uniprot):ASC1
Chain IDs:RB (auth: O)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38011 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0-A
Gene (Uniprot):RPS0A
Chain IDs:SB (auth: P)
Chain Length:219
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P32905 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1-A
Gene (Uniprot):RPS1A
Chain IDs:TB (auth: Q)
Chain Length:214
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P33442 Pfam ID:PF01015

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:UB (auth: R)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P25443 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:VB (auth: S)
Chain Length:260
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

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:WB (auth: T)
Chain Length:226
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX37 Pfam ID:PF01092

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:XB (auth: U)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P26786 Pfam ID:PF01251

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:YB (auth: V)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX39 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:ZB (auth: W)
Chain Length:178
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:O13516 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:AC (auth: X)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX47 Pfam ID:PF16205, PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:BC (auth: Y)
Chain Length:150
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05756 Pfam ID:PF08069, PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-B
Gene (Uniprot):RPS14B
Chain IDs:CC (auth: Z)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P39516 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21-A
Gene (Uniprot):RPS21A
Chain IDs:Z (auth: a)
Chain Length:223
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0C0V8 Pfam ID:PF01249

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Gene (Uniprot):RPS22A
Chain IDs:AA (auth: b)
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0C0W1 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:BA (auth: c)
Chain Length:144
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX29 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:CA (auth: d)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX31 Pfam ID:PF01282

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26-B
Gene (Uniprot):RPS26B
Chain IDs:DA (auth: e)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P39939 Pfam ID:PF01283

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:EA (auth: f)
Chain Length:141
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P35997 Pfam ID:PF01667

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30-A
Gene (Uniprot):RPS30A
Chain IDs:FA (auth: g)
Chain Length:60
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX33 Pfam ID:PF04758

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:HA (auth: l)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:JA (auth: m)
Chain Length:53
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:IA (auth: n)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Protein Blast

Polymer Type:polypeptide(L)
Molecule:5'-3' exoribonuclease 1
Gene (Uniprot):XRN1
Chain IDs:GA (auth: z)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P22147 Pfam ID:PF03159, PF17846, PF18332

Ligand Molecules

Primary Citation

Structure of the 80S ribosome-Xrn1 nuclease complex.

Tesina, P, Heckel, E, Cheng, J, Fromont-Racine, M, Buschauer, R, Kater, L, Beatrix, B, Berninghausen, O, Jacquier, A, Becker, T, Beckmann, R.Show

Nat.Struct.Mol.Biol. 26 275 280 (2019)

PMID: 30911188 DOI: 10.1038/s41594-019-0202-5

Abstact

Messenger RNA (mRNA) homeostasis represents an essential part of gene expression, in which the generation of mRNA by RNA polymerase is counter-balanced by its degradation by nucleases. The conserved 5'-to-3' exoribonuclease Xrn1 has a crucial role in eukaryotic mRNA homeostasis by degrading decapped or cleaved mRNAs post-translationally and, more surprisingly, also co-translationally. Here we report that active Xrn1 can directly and specifically interact with the translation machinery. A cryo-electron microscopy structure of a programmed Saccharomyces cerevisiae 80S ribosome-Xrn1 nuclease complex reveals how the conserved core of Xrn1 enables binding at the mRNA exit site of the ribosome. This interface provides a conduit for channelling of the mRNA from the ribosomal decoding site directly into the active center of the nuclease, thus separating mRNA decoding from degradation by only 17 ± 1 nucleotides. These findings explain how rapid 5'-to-3' mRNA degradation is coupled efficiently to its final round of mRNA translation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures