8T2Y

Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE

  • Classification: RIBOSOME
  • Organism(s): Saccharomyces cerevisiae
  • Mutation(s): No 

  • Deposited: 2023-06-07 Released: 2024-12-11 
  • Deposition Author(s): Zhao, Y., Li, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AA [auth BA]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RPS1A isoform 1B [auth BB]255Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RPS2 isoform 1C [auth BC]254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AD [auth BE]261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AE [auth BG]236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AF [auth BH]190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AG [auth BI]200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AH [auth BJ]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AI [auth BL]156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13J [auth BN]151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AK [auth BO]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AL [auth BV]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RPS22A isoform 1M [auth BW]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AN [auth BX]145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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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 
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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
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RPS3 isoform 1S [auth BD]240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pT [auth BF]225Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AU [auth BK]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RPS15 isoform 1V [auth BP]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AW [auth BQ]143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AX [auth BR]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AY [auth BS]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AZ [auth BT]144Saccharomyces cerevisiaeMutation(s): 0 
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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 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RPS28A isoform 1CA [auth Bc]67Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RPS29A isoform 1DA [auth Bd]56Saccharomyces cerevisiaeMutation(s): 0 
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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 
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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 
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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
RPL10 isoform 1TA [auth AI]221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
RPL11A isoform 1UA [auth AJ]174Saccharomyces cerevisiaeMutation(s): 0 
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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
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AYA [auth AO]199Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AZA [auth AP]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AAB [auth AQ]186Saccharomyces cerevisiaeMutation(s): 0 
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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 
UniProt
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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 
UniProt
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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 
UniProt
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-ARB [auth Ah]120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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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 
UniProt
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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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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3HE
Query on 3HE
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ZD [auth A1]4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
C15 H23 N O4
YPHMISFOHDHNIV-FSZOTQKASA-N
SPD
Query on SPD
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YD [auth A1]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN
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TJ [auth Ao]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AD [auth B5]
AE [auth A1]
AF [auth A1]
AG [auth A1]
AH [auth A1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC		JA [auth AB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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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