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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex.

Wang, J.Wang, J.Shin, B.S.Kim, J.R.Dever, T.E.Puglisi, J.D.Fernandez, I.S.

(2020) Nat Commun 11: 5003-5003

  • DOI: https://doi.org/10.1038/s41467-020-18829-3
  • Primary Citation of Related Structures:  
    6WOO

  • PubMed Abstract: 

    Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNA i Met on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNA i Met immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.


  • Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL2D [auth A]249Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL3E [auth B]384Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL4F [auth C]359Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL18G [auth D]295Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eL6H [auth E]175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL30I [auth F]222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
eL8J [auth G]233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL6K [auth H]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uL16L [auth I]216Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uL5M [auth J]168Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eL13N [auth L]198Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eL14O [auth M]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eL15P [auth N]202Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
uL13Q [auth O]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL22R [auth P]180Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL18S [auth Q]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL19T [auth R]188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
eL20U [auth S]169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL21V [auth T]158Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eL22W [auth U]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL14X [auth V]132Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eL24Y [auth W]62Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uL23Z [auth X]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uL24AA [auth Y]125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eL27BA [auth Z]134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
uL15CA [auth a]147Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eL29DA [auth b]57Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
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eL30EA [auth c]97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL31FA [auth d]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
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eL32GA [auth e]122Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL33HA [auth f]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
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eL34IA [auth g]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
uL29JA [auth h]116Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
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eL36KA [auth i]98Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
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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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Entity ID: 41
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eL40OA [auth m]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL41PA [auth n]23Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
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eL42QA [auth o]101Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL43RA [auth p]87Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
uL1SA [auth q]217Saccharomyces cerevisiaeMutation(s): 0 
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uL10TA [auth r]195Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
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L10UA [auth K]152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
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uS2VA [auth AA]206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
eS1WA [auth BB]214Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
uS5XA [auth CC]217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
uS3YA [auth DD]223Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
eS4ZA [auth EE]257Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
uS7AB [auth FF]206Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
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
MoleculeChains Sequence LengthOrganismDetailsImage
eS7CB [auth HH]184Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
eS8DB [auth II]199Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
uS4EB [auth JJ]182Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05755 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
eS10FB [auth KK]96Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
uS17GB [auth LL]145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
eS12HB [auth MM]124Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
uS15IB [auth NN]150Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uS11JB [auth OO]127Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
uS19KB [auth PP]103Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
uS19LB [auth QQ]141Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
eS17MB [auth RR]123Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P14127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uS13NB [auth SS]136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
eS19OB [auth TT]143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
uS10PB [auth UU]106Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
eS21QB [auth VV]87Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
uS8RB [auth WW]129Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
uS12SB [auth XX]144Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
eS24TB [auth YY]134Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
eS25UB [auth ZZ]70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ3E792
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
eS26VB [auth aa]97Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
eS27WB [auth bb]81Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
eS28XB [auth cc]63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
uS14YB [auth dd]53Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
eS30ZB [auth ee]53Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
eS31AC [auth ff]57Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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