Skip to main content

 6FYY | pdb_00006fyy

Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6FYY

This is version 1.4 of the entry. See complete history. 

Literature

Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.

Llacer, J.L., Hussain, T., Saini, A.K., Nanda, J.D., Kaur, S., Gordiyenko, Y., Kumar, R., Hinnebusch, A.G., Lorsch, J.R., Ramakrishnan, V.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.39273
  • Primary Citation Related Structures: 
    6FYX, 6FYY

  • PubMed Abstract: 

    In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNA i in a 'P IN ' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a yeast 48S pre-initiation complex (PIC), at an overall resolution of 3.0 Å, featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNA i . Substitutions of eIF5 residues involved in the eIF5-NTD/tRNA i interaction influenced initiation at near-cognate UUG codons in vivo, and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection.


  • Organizational Affiliation: 
    • MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 1,762.41 kDa 
  • Atom Count: 104,316 
  • Modeled Residue Count: 10,028 
  • Deposited Residue Count: 12,070 
  • Unique protein chains: 44
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S0D [auth A]254Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CN12 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CN12 
Go to UniProtKB:  Q6CN12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CN12
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S1E [auth B]255Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CWD0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CWD0 
Go to UniProtKB:  Q6CWD0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CWD0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0F09812pF [auth C]259Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0D08305pG [auth D]237Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4H [auth E]261Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0D10659pI [auth F]227Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6J [auth G]236Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CM04 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CM04 
Go to UniProtKB:  Q6CM04
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CM04
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S7K [auth H]190Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8L [auth I]201Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0E23673pM [auth J]188Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0B08173pN [auth K]106Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0A10483pO [auth L]156Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S12P [auth M]134Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0F18040pQ [auth N]151Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14R [auth O]137Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P27069 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore P27069 
Go to UniProtKB:  P27069
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27069
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0F07843pS [auth P]142Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S16T [auth Q]143Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q875N2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q875N2 
Go to UniProtKB:  Q875N2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ875N2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0B01474pU [auth R]136Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0B01562pV [auth S]146Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0A07194pW [auth T]144Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0F25542pX [auth U]117Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Y [auth V]87Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CXT6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CXT6 
Go to UniProtKB:  Q6CXT6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CXT6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S22Z [auth W]130Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CW21 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CW21 
Go to UniProtKB:  Q6CW21
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CW21
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0B11231pAA [auth X]145Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S24BA [auth Y]135Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0B06182pCA [auth Z]108Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S26DA [auth a]119Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27EA [auth b]82Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S28FA [auth c]67Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P33285 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore P33285 
Go to UniProtKB:  P33285
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33285
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S29GA [auth d]56Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CPG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CPG3 
Go to UniProtKB:  Q6CPG3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CPG3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30HA [auth e]63Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aIA [auth f]150Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P69061 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore P69061 
Go to UniProtKB:  P69061
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69061
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0E12277pJA [auth g]326Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AKA [auth h]25Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX86 
Go to UniProtKB:  P0CX86
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX86
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1ALA [auth i]153Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TIF11, YMR260C, YM8156.02C
UniProt
Find proteins for P38912 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38912 
Go to UniProtKB:  P38912
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38912
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit alphaMA [auth j]304Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUI2, TIF211, YJR007W, J1429
UniProt
Find proteins for P20459 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20459 
Go to UniProtKB:  P20459
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20459
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit gammaNA [auth k]527Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD11, TIF213, YER025W
EC: 3.6.5.3
UniProt
Find proteins for P32481 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32481 
Go to UniProtKB:  P32481
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32481
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit betaOA [auth l]285Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUI3, TIF212, YPL237W
UniProt
Find proteins for P09064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P09064 
Go to UniProtKB:  P09064
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09064
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5PA [auth m]405Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TIF5, YPR041W, YP3085.05
UniProt
Find proteins for P38431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38431 
Go to UniProtKB:  P38431
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38431
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit AQA [auth o]964Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPG1, TIF32, YBR079C, YBR0734
UniProt
Find proteins for P38249 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38249 
Go to UniProtKB:  P38249
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38249
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit BRA [auth p]763Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRT1, CDC63, YOR361C
UniProt
Find proteins for P06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06103 
Go to UniProtKB:  P06103
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06103
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
eIF3c,Eukaryotic translation initiation factor 3 subunit CSA [auth q]812Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32497 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32497 
Go to UniProtKB:  P32497
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32497
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit GTA [auth r]274Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TIF35, SCY_1313
UniProt
Find proteins for A6ZZ25 (Saccharomyces cerevisiae (strain YJM789))
Explore A6ZZ25 
Go to UniProtKB:  A6ZZ25
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6ZZ25
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit IUA [auth s]347Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TIF34, SCY_4321
UniProt
Find proteins for A6ZMK5 (Saccharomyces cerevisiae (strain YJM789))
Explore A6ZMK5 
Go to UniProtKB:  A6ZMK5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6ZMK5
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
tRNAiA [auth 1]76Saccharomyces cerevisiae
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
18S ribosomal RNAB [auth 2]1,798Kluyveromyces lactis NRRL Y-1140
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
mRNA (31-MER)C [auth 3]49Saccharomyces cerevisiae
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on GCP



Download:Ideal Coordinates CCD File
MF [auth k]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
MET

Query on MET



Download:Ideal Coordinates CCD File
KF [auth k]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
HF [auth a],
IF [auth b],
JF [auth f],
NF [auth l],
OF [auth m]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AB [auth 2]
AC [auth 2]
AD [auth 2]
AE [auth 2]
AF [auth 2]
AB [auth 2],
AC [auth 2],
AD [auth 2],
AE [auth 2],
AF [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
BE [auth 2],
BF [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
CE [auth 2],
CF [auth 2],
DB [auth 2],
DC [auth 2],
DD [auth 2],
DE [auth 2],
DF [auth 2],
EB [auth 2],
EC [auth 2],
ED [auth 2],
EE [auth 2],
EF [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
FE [auth 2],
FF [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
GE [auth 2],
GF [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
HE [auth 2],
IB [auth 2],
IC [auth 2],
ID [auth 2],
IE [auth 2],
JB [auth 2],
JC [auth 2],
JD [auth 2],
JE [auth 2],
KB [auth 2],
KC [auth 2],
KD [auth 2],
KE [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
LE [auth 2],
LF [auth k],
MB [auth 2],
MC [auth 2],
MD [auth 2],
ME [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
NE [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
OE [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
PE [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
QE [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
RE [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth 2],
SE [auth 2],
TB [auth 2],
TC [auth 2],
TD [auth 2],
TE [auth 2],
UB [auth 2],
UC [auth 2],
UD [auth 2],
UE [auth 2],
VA [auth 2],
VB [auth 2],
VC [auth 2],
VD [auth 2],
VE [auth 2],
WA [auth 2],
WB [auth 2],
WC [auth 2],
WD [auth 2],
WE [auth 2],
XA [auth 2],
XB [auth 2],
XC [auth 2],
XD [auth 2],
XE [auth 2],
YA [auth 2],
YB [auth 2],
YC [auth 2],
YD [auth 2],
YE [auth 2],
ZA [auth 2],
ZB [auth 2],
ZC [auth 2],
ZD [auth 2],
ZE [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Non-standard Monomers  2 Unique
IDChains TypeFormula2D Diagram
UNK
Query on UNK
L-PEPTIDE LINKINGC4 H9 N O2
AYA
Query on AYA
L-PEPTIDE LINKINGC5 H9 N O3

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTREFMAC5.8

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
FEBSUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-07-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Other
  • Version 1.4: 2024-04-24
    Changes: Data collection, Database references, Derived calculations, Refinement description