6WOO

CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

An active role of the eukaryotic large ribosomal subunit in translation initiation fidelity.

Wang, J.Wang, J.Puglisi, J.Fernandez, I.S.

To be published.

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Entity ID: 4
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uL2D [auth A]249Saccharomyces cerevisiaeMutation(s): 0 
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uL3E [auth B]384Saccharomyces cerevisiaeMutation(s): 0 
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uL4F [auth C]359Saccharomyces cerevisiaeMutation(s): 0 
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uL18G [auth D]295Saccharomyces cerevisiaeMutation(s): 0 
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eL6H [auth E]175Saccharomyces cerevisiaeMutation(s): 0 
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uL30I [auth F]222Saccharomyces cerevisiaeMutation(s): 0 
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eL8J [auth G]233Saccharomyces cerevisiaeMutation(s): 0 
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uL6K [auth H]191Saccharomyces cerevisiaeMutation(s): 0 
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uL16L [auth I]216Saccharomyces cerevisiaeMutation(s): 0 
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uL5M [auth J]168Saccharomyces cerevisiaeMutation(s): 0 
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eL13N [auth L]198Saccharomyces cerevisiaeMutation(s): 0 
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eL14O [auth M]136Saccharomyces cerevisiaeMutation(s): 0 
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eL15P [auth N]202Saccharomyces cerevisiaeMutation(s): 0 
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uL13Q [auth O]197Saccharomyces cerevisiaeMutation(s): 0 
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uL22R [auth P]180Saccharomyces cerevisiaeMutation(s): 0 
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eL18S [auth Q]184Saccharomyces cerevisiaeMutation(s): 0 
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eL19T [auth R]188Saccharomyces cerevisiaeMutation(s): 0 
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eL20U [auth S]169Saccharomyces cerevisiaeMutation(s): 0 
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eL21V [auth T]158Saccharomyces cerevisiaeMutation(s): 0 
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eL22W [auth U]100Saccharomyces cerevisiaeMutation(s): 0 
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uL14X [auth V]132Saccharomyces cerevisiaeMutation(s): 0 
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eL24Y [auth W]62Saccharomyces cerevisiaeMutation(s): 0 
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uL23Z [auth X]121Saccharomyces cerevisiaeMutation(s): 0 
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uL24AA [auth Y]125Saccharomyces cerevisiaeMutation(s): 0 
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eL27BA [auth Z]134Saccharomyces cerevisiaeMutation(s): 0 
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uL15CA [auth a]147Saccharomyces cerevisiaeMutation(s): 0 
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eL29DA [auth b]57Saccharomyces cerevisiaeMutation(s): 0 
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eL30EA [auth c]97Saccharomyces cerevisiaeMutation(s): 0 
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eL31FA [auth d]106Saccharomyces cerevisiaeMutation(s): 0 
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eL32GA [auth e]122Saccharomyces cerevisiaeMutation(s): 0 
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eL33HA [auth f]105Saccharomyces cerevisiaeMutation(s): 0 
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eL34IA [auth g]121Saccharomyces cerevisiaeMutation(s): 0 
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uL29JA [auth h]116Saccharomyces cerevisiaeMutation(s): 0 
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eL36KA [auth i]98Saccharomyces cerevisiaeMutation(s): 0 
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eL37LA [auth j]85Saccharomyces cerevisiaeMutation(s): 0 
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eL38MA [auth k]76Saccharomyces cerevisiaeMutation(s): 0 
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eL39NA [auth l]49Saccharomyces cerevisiaeMutation(s): 0 
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eL40OA [auth m]51Saccharomyces cerevisiaeMutation(s): 0 
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eL41PA [auth n]23Saccharomyces cerevisiaeMutation(s): 0 
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eL42QA [auth o]101Saccharomyces cerevisiaeMutation(s): 0 
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eL43RA [auth p]87Saccharomyces cerevisiaeMutation(s): 0 
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uL1SA [auth q]217Saccharomyces cerevisiaeMutation(s): 0 
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uL10TA [auth r]195Saccharomyces cerevisiaeMutation(s): 0 
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L10UA [auth K]152Saccharomyces cerevisiaeMutation(s): 0 
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uS2VA [auth AA]206Saccharomyces cerevisiaeMutation(s): 0 
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eS1WA [auth BB]214Saccharomyces cerevisiaeMutation(s): 0 
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uS5XA [auth CC]217Saccharomyces cerevisiaeMutation(s): 0 
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uS3YA [auth DD]223Saccharomyces cerevisiaeMutation(s): 0 
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eS4ZA [auth EE]257Saccharomyces cerevisiaeMutation(s): 0 
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uS7AB [auth FF]206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS5PACBIOSEQ_LOCUS3372PACBIOSEQ_LOCUS3390PACBIOSEQ_LOCUS3391PACBIOSEQ_LOCUS3422PACBIOSEQ_LOCUS3460SCNYR20_0009028700SCP684_0009028200
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Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 54
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eS6BB [auth GG]226Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
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eS7CB [auth HH]184Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 56
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eS8DB [auth II]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
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uS4EB [auth JJ]182Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 58
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eS10FB [auth KK]96Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
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uS17GB [auth LL]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
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eS12HB [auth MM]124Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
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uS15IB [auth NN]150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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uS11JB [auth OO]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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uS19KB [auth PP]103Saccharomyces cerevisiaeMutation(s): 0 
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uS19LB [auth QQ]141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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eS17MB [auth RR]123Saccharomyces cerevisiaeMutation(s): 0 
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uS13NB [auth SS]136Saccharomyces cerevisiaeMutation(s): 0 
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eS19OB [auth TT]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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uS10PB [auth UU]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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eS21QB [auth VV]87Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
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uS8RB [auth WW]129Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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uS12SB [auth XX]144Saccharomyces cerevisiaeMutation(s): 0 
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eS24TB [auth YY]134Saccharomyces cerevisiaeMutation(s): 0 
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eS25UB [auth ZZ]70Saccharomyces cerevisiaeMutation(s): 0 
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eS26VB [auth aa]97Saccharomyces cerevisiaeMutation(s): 0 
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eS27WB [auth bb]81Saccharomyces cerevisiaeMutation(s): 0 
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eS28XB [auth cc]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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uS14YB [auth dd]53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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eS30ZB [auth ee]53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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eS31AC [auth ff]57Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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RACK1BC [auth gg]318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
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eIF5BDC [auth 1]600Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: FUN12YAL035W
EC: 3.6.5.3
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Entity ID: 1
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25S ribosomal RNAA [auth 5]3271Saccharomyces cerevisiae
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Entity ID: 2
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5S ribosomal RNAB [auth 7]121Saccharomyces cerevisiae
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Entity ID: 3
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5.8S ribosomal rRNAC [auth 8]157Saccharomyces cerevisiae
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Entity ID: 81
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18S ribosomal RNACC [auth 2]1796Saccharomyces cerevisiae
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Entity ID: 83
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Met-tRNA-iMetEC [auth 3]76Saccharomyces cerevisiae
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Entity ID: 84
MoleculeChainsLengthOrganismImage
mRNAFC [auth 4]6Saccharomyces cerevisiae
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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MC [auth 1]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
U6A
Query on U6A

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NC [auth 3]N-carboxy-L-threonine
C5 H9 N O5
OJLPTWSLDBSLEH-GBXIJSLDSA-N
 Ligand Interaction
MET
Query on MET

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OC [auth 3]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

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GC [auth j],
HC [auth m],
IC [auth o],
JC [auth aa],
KC [auth bb],
GC [auth j],
HC [auth m],
IC [auth o],
JC [auth aa],
KC [auth bb],
LC [auth ff]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release