8EWB image
Deposition Date 2022-10-22
Release Date 2023-09-06
Last Version Date 2024-12-25
Entry Detail
PDB ID:
8EWB
Keywords:
RIBOSOME
Title:
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III
Biological Source:
Source Organism:
Taura syndrome virus (Taxon ID: 142102)
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.87 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8EWB validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:LA (auth: A1)
Chain Length:3360
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5s rRNA
Chain IDs:MA (auth: A3)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5.8 S rRNA
Chain IDs:NA (auth: A4)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:IA (auth: AA)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:JA (auth: AB)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14126 Pfam ID:PF00297
Polymer Type:polypeptide(L)
Molecule:RPL4A isoform 1
Chain IDs:KA (auth: AC)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL5 isoform 1
Chain IDs:OA (auth: AD)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:PA (auth: AE)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02326 Pfam ID:PF01159
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:QA (auth: AF)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:RA (auth: AG)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:SA (auth: AH)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05738 Pfam ID:PF00347
Polymer Type:polypeptide(L)
Molecule:RPL10 isoform 1
Chain IDs:TA (auth: AI)
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL11A isoform 1
Chain IDs:UA (auth: AJ)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:VA (auth: AL)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12690 Pfam ID:PF01294
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:WA (auth: AM)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:XA (auth: AN)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05748 Pfam ID:PF00827
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:YA (auth: AO)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26784 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:ZA (auth: AP)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05740 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:AB (auth: AQ)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX49 Pfam ID:PF17135
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:BB (auth: AR)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX82 Pfam ID:PF01280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20
Gene (Uniprot):SCRG_02137
Chain IDs:CB (auth: AS)
Chain Length:178
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:B3LMD0 Pfam ID:PF01775
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:DB (auth: AT)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02753 Pfam ID:PF01157
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:EB (auth: AU)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05749 Pfam ID:PF01776
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:FB (auth: AV)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX41 Pfam ID:PF00238
Polymer Type:polypeptide(L)
Molecule:RPL24A isoform 1
Chain IDs:GB (auth: AW)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:HB (auth: AX)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:IB (auth: AY)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:JB (auth: AZ)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H6 Pfam ID:PF01777
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:KB (auth: Aa)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02406 Pfam ID:PF00828
Polymer Type:polypeptide(L)
Molecule:RPL29 isoform 1
Chain IDs:LB (auth: Ab)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:MB (auth: Ac)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14120 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:NB (auth: Ad)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H8 Pfam ID:PF01198
Polymer Type:polypeptide(L)
Molecule:RPL32 isoform 1
Chain IDs:OB (auth: Ae)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:PB (auth: Af)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05744 Pfam ID:PF01247
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:QB (auth: Ag)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P87262 Pfam ID:PF01199
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:RB (auth: Ah)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX84 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:SB (auth: Ai)
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05745 Pfam ID:PF01158
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:TB (auth: Aj)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49166 Pfam ID:PF01907
Polymer Type:polypeptide(L)
Molecule:RPL38 isoform 1
Chain IDs:UB (auth: Ak)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:VB (auth: Al)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04650 Pfam ID:PF00832
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):RPL40A
Chain IDs:WB (auth: Am)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CH08 Pfam ID:PF00240, PF01020
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-A
Gene (Uniprot):RPL41A
Chain IDs:XB (auth: An)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX86 Pfam ID:PF05162
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:YB (auth: Ao)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX27 Pfam ID:PF00935
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:ZB (auth: Ap)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX25 Pfam ID:PF01780
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:HA (auth: B5)
Chain Length:1798
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0-A
Gene (Uniprot):RPS0A
Chain IDs:A (auth: BA)
Chain Length:252
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32905 Pfam ID:PF00318
Polymer Type:polypeptide(L)
Molecule:RPS1A isoform 1
Chain IDs:B (auth: BB)
Chain Length:255
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS2 isoform 1
Chain IDs:C (auth: BC)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS3 isoform 1
Chain IDs:S (auth: BD)
Chain Length:240
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:D (auth: BE)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX35 Pfam ID:PF00900, PF16121, PF08071, PF01479, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rps5p
Gene (Uniprot):RPS5
Chain IDs:T (auth: BF)
Chain Length:225
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:A0A1L4AA68 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:E (auth: BG)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX37 Pfam ID:PF01092
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:F (auth: BH)
Chain Length:190
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26786 Pfam ID:PF01251
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:G (auth: BI)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX39 Pfam ID:PF01201
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:H (auth: BJ)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A
Gene (Uniprot):RPS10A
Chain IDs:U (auth: BK)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08745 Pfam ID:PF03501
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:I (auth: BL)
Chain Length:156
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX47 Pfam ID:PF16205, PF00366
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Chain IDs:GA (auth: BM)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:J (auth: BN)
Chain Length:151
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05756 Pfam ID:PF08069, PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Gene (Uniprot):RPS14A
Chain IDs:K (auth: BO)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06367 Pfam ID:PF00411
Polymer Type:polypeptide(L)
Molecule:RPS15 isoform 1
Chain IDs:V (auth: BP)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:W (auth: BQ)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX51 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17-A
Gene (Uniprot):RPS17A
Chain IDs:X (auth: BR)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02407 Pfam ID:PF00833
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-A
Gene (Uniprot):RPS18A
Chain IDs:Y (auth: BS)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX55 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19-A
Gene (Uniprot):RPS19A
Chain IDs:Z (auth: BT)
Chain Length:144
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P07280 Pfam ID:PF01090
Polymer Type:polypeptide(L)
Molecule:RPS20 isoform 1
Chain IDs:AA (auth: BU)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21-A
Gene (Uniprot):RPS21A
Chain IDs:L (auth: BV)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0V8 Pfam ID:PF01249
Polymer Type:polypeptide(L)
Molecule:RPS22A isoform 1
Chain IDs:M (auth: BW)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:N (auth: BX)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX29 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:O (auth: BY)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX31 Pfam ID:PF01282
Polymer Type:polypeptide(L)
Molecule:RPS25A isoform 1
Chain IDs:BA (auth: BZ)
Chain Length:108
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS26B isoform 1
Chain IDs:P (auth: Ba)
Chain Length:252
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:Q (auth: Bb)
Chain Length:255
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P35997 Pfam ID:PF01667
Polymer Type:polypeptide(L)
Molecule:RPS28A isoform 1
Chain IDs:CA (auth: Bc)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS29A isoform 1
Chain IDs:DA (auth: Bd)
Chain Length:240
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30-A
Gene (Uniprot):RPS30A
Chain IDs:R (auth: Be)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX33 Pfam ID:PF04758
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31
Chain IDs:FA (auth: Bf)
Chain Length:225
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-like protein
Gene (Uniprot):ASC1
Chain IDs:EA (auth: Bg)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38011 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Elongation factor 2
Gene (Uniprot):EFT1, EFT2
Chain IDs:BC (auth: DC)
Chain Length:842
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32324 Pfam ID:PF00009, PF03144, PF14492, PF03764, PF00679
Polymer Type:polypeptide(L)
Molecule:RPL1A isoform 1
Chain IDs:AC (auth: E)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:Taura syndrome virus (TSV) internal ribosome entry site (IRES) RNA
Chain IDs:DC (auth: EC)
Chain Length:202
Number of Molecules:1
Biological Source:Taura syndrome virus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Gene (Uniprot):RPP0
Chain IDs:CC (auth: V)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05317 Pfam ID:PF00466, PF17777, PF00428
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A2M HA A modified residue
DDE BC HIS modified residue
G7M HA G modified residue
HIC JA HIS modified residue
MA6 HA A modified residue
OMC HA C modified residue
OMG HA G modified residue
OMU HA U modified residue
Ligand Molecules
GDP
MG
ZN
Primary Citation
Regulation of translation by ribosomal RNA pseudouridylation.
Sci Adv 9 eadg8190 eadg8190 (2023)
PMID: 37595043 DOI: 10.1126/sciadv.adg8190

Abstact

Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
8EWB