5OA3

Human 40S-eIF2D-re-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and Functional Insights into Human Re-initiation Complexes.

Weisser, M.Schafer, T.Leibundgut, M.Bohringer, D.Aylett, C.H.S.Ban, N.

(2017) Mol Cell 67: 447-456.e7

  • DOI: 10.1016/j.molcel.2017.06.032
  • Primary Citation of Related Structures:  
    5OA9, 5OA3

  • PubMed Abstract: 
  • After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which ar ...

    After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which are important in cancer. Key ribosomal binding proteins involved in re-initiation are the eukaryotic translation initiation factor 2D (eIF2D) or the homologous complex of MCT-1/DENR. We determined the structures of these factors bound to the human 40S ribosomal subunit in complex with initiator tRNA positioned on an mRNA start codon in the P-site using a combination of cryoelectron microscopy and X-ray crystallography. The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2D0584Homo sapiensMutation(s): 0 
Gene Names: EIF2DHCA56LGTN
Find proteins for P41214 (Homo sapiens)
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PHAROS  P41214
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAA295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
Find proteins for P08865 (Homo sapiens)
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PHAROS  P08865
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aB264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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PHAROS  P61247
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2C293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
Find proteins for P15880 (Homo sapiens)
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PHAROS  P15880
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3D243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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PHAROS  P23396
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
Find proteins for P62701 (Homo sapiens)
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PHAROS  P62701
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5F204Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
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PHAROS  P46782
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6G249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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PHAROS  P62753
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7H194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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PHAROS  P62081
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8I208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
Find proteins for P62241 (Homo sapiens)
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PHAROS  P62241
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9J194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10K165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11L158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12M132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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PHAROS  P25398
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13N151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14O151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15P145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16Q146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
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PHAROS  P62249
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17R135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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PHAROS  P08708
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18S152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
Find proteins for P62269 (Homo sapiens)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19T145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20U119Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21V83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aW130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
Find proteins for P62244 (Homo sapiens)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23X143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24Y130Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25Z125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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PHAROS  P62851
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26a101Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27b82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28c61Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29d55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30e56Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S27af72Homo sapiensMutation(s): 0 
Gene Names: RPS27A
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1g315Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN EL41h24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 2
MoleculeChainsLengthOrganismImage
initiator Met-tRNA-i175Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChainsLengthOrganismImage
18S ribosomal RNA21868Homo sapiens
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Entity ID: 4
MoleculeChainsLengthOrganismImage
IRES mRNA3275Hepacivirus C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
a, d, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Other