8T3B | pdb_00008t3b

Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

Regulation of Translation by Ribosome RNA 2'-O-Methylation

Zhao, Y., Li, H.

To be published.

Macromolecule Content 

  • Total Structure Weight: 3,279.04 kDa 
  • Atom Count: 212,418 
  • Modeled Residue Count: 17,572 
  • Deposited Residue Count: 18,585 
  • Unique protein chains: 76
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AA [auth BA]252Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS1A isoform 1B [auth BB]255Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS2 isoform 1C [auth BC]254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AD [auth BE]261Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AE [auth BG]236Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AF [auth BH]190Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AG [auth BI]200Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AH [auth BJ]197Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AI [auth BL]156Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13J [auth BN]151Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AK [auth BO]137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AL [auth BV]87Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS22A isoform 1M [auth BW]130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AN [auth BX]145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AO [auth BY]135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS26B isoform 1P [auth Ba]119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AQ [auth Bb]82Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AR [auth Be]63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS3 isoform 1S [auth BD]240Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Rps5pT [auth BF]225Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AU [auth BK]105Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS15 isoform 1V [auth BP]142Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AW [auth BQ]143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AX [auth BR]136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AY [auth BS]146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AZ [auth BT]144Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS20 isoform 1AA [auth BU]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS25A isoform 1BA [auth BZ]108Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS28A isoform 1CA [auth Bc]67Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
RPS29A isoform 1DA [auth Bd]56Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinEA [auth Bg]319Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31FA [auth Bf]152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S12GA [auth BM]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AIA [auth AA]254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L3JA [auth AB]387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
RPL4A isoform 1KA [auth AC]362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
RPL5 isoform 1OA [auth AD]297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-APA [auth AE]176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AQA [auth AF]244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-ARA [auth AG]256Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-ASA [auth AH]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L10TA [auth AI]222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
RPL11A isoform 1UA [auth AJ]174Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AVA [auth AL]199Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AWA [auth AM]138Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AXA [auth AN]204Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AYA [auth AO]199Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AZA [auth AP]184Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AAB [auth AQ]186Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-ABB [auth AR]189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L20CB [auth AS]178Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-ADB [auth AT]160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AEB [auth AU]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AFB [auth AV]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
RPL24A isoform 1GB [auth AW]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L25HB [auth AX]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AIB [auth AY]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AJB [auth AZ]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28KB [auth Aa]149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChains  Sequence LengthOrganismDetailsImage
RPL29 isoform 1LB [auth Ab]59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L30MB [auth Ac]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-ANB [auth Ad]113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains  Sequence LengthOrganismDetailsImage
RPL32 isoform 1OB [auth Ae]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-APB [auth Af]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AQB [auth Ag]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-ARB [auth Ah]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ASB [auth Ai]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ATB [auth Aj]88Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains  Sequence LengthOrganismDetailsImage
RPL38 isoform 1UB [auth Ak]78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L39VB [auth Al]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40WB [auth Am]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AXB [auth An]25Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AYB [auth Ao]106Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AZB [auth Ap]92Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains  Sequence LengthOrganismDetailsImage
RPL1A isoform 1AC [auth E]217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor 2BC [auth DC]842Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.5
UniProt
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Entity ID: 34
MoleculeChains LengthOrganismImage
18S rRNAHA [auth B5]1,798Saccharomyces cerevisiae
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Entity ID: 38
MoleculeChains LengthOrganismImage
25S rRNALA [auth A1]3,360Saccharomyces cerevisiae
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Entity ID: 39
MoleculeChains LengthOrganismImage
5s rRNAMA [auth A3]121Saccharomyces cerevisiae
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Entity ID: 40
MoleculeChains LengthOrganismImage
5.8 S rRNANA [auth A4]158Saccharomyces cerevisiae
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Entity ID: 81
MoleculeChains LengthOrganismImage
TSV IRESCC [auth EC]202Taura syndrome virus
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Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO1

Query on SO1


Download:Ideal Coordinates CCD File
GC [auth DC][1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID
C27 H42 O8
DIBGPTPYRVEPSP-OHFCZZTFSA-N
GDP

Query on GDP


Download:Ideal Coordinates CCD File
EC [auth DC]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
DC [auth Ao]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
FC [auth DC]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC		JA [auth AB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
DDE
Query on DDE		BC [auth DC]L-PEPTIDE LINKINGC13 H24 N5 O3HIS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124622

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release