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:  
    5OA3, 5OA9

  • 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 are important in cancer ...

    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 2DA [auth 0]584Homo sapiensMutation(s): 0 
Gene Names: EIF2DHCA56LGTN
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAE [auth A]295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aF [auth B]264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2G [auth C]293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3H [auth D]243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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Entity ID: 9
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40S ribosomal protein S4, X isoformI [auth E]263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 10
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40S ribosomal protein S5J [auth F]204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 11
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40S ribosomal protein S6K [auth G]249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 12
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40S ribosomal protein S7L [auth H]194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 13
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40S ribosomal protein S8M [auth I]208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 14
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40S ribosomal protein S9N [auth J]194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 15
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40S ribosomal protein S10O [auth K]165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 16
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40S ribosomal protein S11P [auth L]158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 17
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40S ribosomal protein S12Q [auth M]132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 18
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40S ribosomal protein S13R [auth N]151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 19
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40S ribosomal protein S14S [auth O]151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 20
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40S ribosomal protein S15T [auth P]145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 21
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40S ribosomal protein S16U [auth Q]146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 22
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40S ribosomal protein S17V [auth R]135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 23
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40S ribosomal protein S18W [auth S]152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 24
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40S ribosomal protein S19X [auth T]145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 25
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40S ribosomal protein S20Y [auth U]119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 26
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40S ribosomal protein S21Z [auth V]83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aAA [auth W]130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 28
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40S ribosomal protein S23BA [auth X]143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 29
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40S ribosomal protein S24CA [auth Y]130Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 30
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40S ribosomal protein S25DA [auth Z]125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 31
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40S ribosomal protein S26EA [auth a]101Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 32
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40S ribosomal protein S27FA [auth b]82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 33
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40S ribosomal protein S28GA [auth c]61Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 34
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40S ribosomal protein S29HA [auth d]55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 35
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40S ribosomal protein S30IA [auth e]56Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 36
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Ribosomal protein S27aJA [auth f]72Homo sapiensMutation(s): 0 
Gene Names: RPS27A
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Entity ID: 37
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Receptor of activated protein C kinase 1KA [auth g]315Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN EL41LA [auth h]24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 2
MoleculeChainsLengthOrganismImage
initiator Met-tRNA-iB [auth 1]75Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChainsLengthOrganismImage
18S ribosomal RNAC [auth 2]1,868Homo sapiens
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Entity ID: 4
MoleculeChainsLengthOrganismImage
IRES mRNAD [auth 3]275Hepacivirus C
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
MA [auth a],
NA [auth d],
OA [auth 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 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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