5OA3

Human 40S-eIF2D-re-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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.,Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2D
0
584Homo sapiensMutation(s): 0 
Gene Names: EIF2D (HCA56, LGTN)
Find proteins for P41214 (Homo sapiens)
Go to Gene View: EIF2D
Go to UniProtKB:  P41214
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
A
295Homo sapiensMutation(s): 0 
Gene Names: RPSA (LAMBR, LAMR1)
Find proteins for P08865 (Homo sapiens)
Go to Gene View: RPSA
Go to UniProtKB:  P08865
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
B
264Homo sapiensMutation(s): 0 
Gene Names: RPS3A (FTE1, MFTL)
Find proteins for P61247 (Homo sapiens)
Go to Gene View: RPS3A
Go to UniProtKB:  P61247
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
C
293Homo sapiensMutation(s): 0 
Gene Names: RPS2 (RPS4)
Find proteins for P15880 (Homo sapiens)
Go to Gene View: RPS2
Go to UniProtKB:  P15880
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
D
243Homo sapiensMutation(s): 0 
Gene Names: RPS3
EC: 4.2.99.18
Find proteins for P23396 (Homo sapiens)
Go to Gene View: RPS3
Go to UniProtKB:  P23396
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4, X isoform
E
263Homo sapiensMutation(s): 0 
Gene Names: RPS4X (CCG2, RPS4, SCAR)
Find proteins for P62701 (Homo sapiens)
Go to Gene View: RPS4X
Go to UniProtKB:  P62701
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
F
204Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
Go to Gene View: RPS5
Go to UniProtKB:  P46782
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
G
249Homo sapiensMutation(s): 0 
Gene Names: RPS6
Find proteins for P62753 (Homo sapiens)
Go to Gene View: RPS6
Go to UniProtKB:  P62753
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
H
194Homo sapiensMutation(s): 0 
Gene Names: RPS7
Find proteins for P62081 (Homo sapiens)
Go to Gene View: RPS7
Go to UniProtKB:  P62081
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
I
208Homo sapiensMutation(s): 0 
Gene Names: RPS8
Find proteins for P62241 (Homo sapiens)
Go to Gene View: RPS8
Go to UniProtKB:  P62241
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9
J
194Homo sapiensMutation(s): 0 
Gene Names: RPS9
Find proteins for P46781 (Homo sapiens)
Go to Gene View: RPS9
Go to UniProtKB:  P46781
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10
K
165Homo sapiensMutation(s): 0 
Gene Names: RPS10
Find proteins for P46783 (Homo sapiens)
Go to Gene View: RPS10
Go to UniProtKB:  P46783
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
L
158Homo sapiensMutation(s): 0 
Gene Names: RPS11
Find proteins for P62280 (Homo sapiens)
Go to Gene View: RPS11
Go to UniProtKB:  P62280
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
M
132Homo sapiensMutation(s): 0 
Gene Names: RPS12
Find proteins for P25398 (Homo sapiens)
Go to Gene View: RPS12
Go to UniProtKB:  P25398
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
N
151Homo sapiensMutation(s): 0 
Gene Names: RPS13
Find proteins for P62277 (Homo sapiens)
Go to Gene View: RPS13
Go to UniProtKB:  P62277
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
O
151Homo sapiensMutation(s): 0 
Gene Names: RPS14
Find proteins for P62263 (Homo sapiens)
Go to Gene View: RPS14
Go to UniProtKB:  P62263
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
P
145Homo sapiensMutation(s): 0 
Gene Names: RPS15 (RIG)
Find proteins for P62841 (Homo sapiens)
Go to Gene View: RPS15
Go to UniProtKB:  P62841
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
Q
146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
Go to Gene View: RPS16
Go to UniProtKB:  P62249
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17
R
135Homo sapiensMutation(s): 0 
Gene Names: RPS17 (RPS17L)
Find proteins for P08708 (Homo sapiens)
Go to Gene View: RPS17
Go to UniProtKB:  P08708
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
S
152Homo sapiensMutation(s): 0 
Gene Names: RPS18 (D6S218E)
Find proteins for P62269 (Homo sapiens)
Go to Gene View: RPS18
Go to UniProtKB:  P62269
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
T
145Homo sapiensMutation(s): 0 
Gene Names: RPS19
Find proteins for P39019 (Homo sapiens)
Go to Gene View: RPS19
Go to UniProtKB:  P39019
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
U
119Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
Go to Gene View: RPS20
Go to UniProtKB:  P60866
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
V
83Homo sapiensMutation(s): 0 
Gene Names: RPS21
Find proteins for P63220 (Homo sapiens)
Go to Gene View: RPS21
Go to UniProtKB:  P63220
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15a
W
130Homo sapiensMutation(s): 0 
Gene Names: RPS15A
Find proteins for P62244 (Homo sapiens)
Go to Gene View: RPS15A
Go to UniProtKB:  P62244
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
X
143Homo sapiensMutation(s): 0 
Gene Names: RPS23
Find proteins for P62266 (Homo sapiens)
Go to Gene View: RPS23
Go to UniProtKB:  P62266
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
Y
130Homo sapiensMutation(s): 0 
Gene Names: RPS24
Find proteins for P62847 (Homo sapiens)
Go to Gene View: RPS24
Go to UniProtKB:  P62847
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25
Z
125Homo sapiensMutation(s): 0 
Gene Names: RPS25
Find proteins for P62851 (Homo sapiens)
Go to Gene View: RPS25
Go to UniProtKB:  P62851
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26
a
101Homo sapiensMutation(s): 0 
Gene Names: RPS26
Find proteins for P62854 (Homo sapiens)
Go to Gene View: RPS26
Go to UniProtKB:  P62854
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
b
82Homo sapiensMutation(s): 0 
Gene Names: RPS27 (MPS1)
Find proteins for P42677 (Homo sapiens)
Go to Gene View: RPS27
Go to UniProtKB:  P42677
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28
c
61Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
Go to Gene View: RPS28
Go to UniProtKB:  P62857
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29
d
55Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
Go to Gene View: RPS29
Go to UniProtKB:  P62273
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
e
56Homo sapiensMutation(s): 0 
Gene Names: FAU
Find proteins for P62861 (Homo sapiens)
Go to Gene View: FAU
Go to UniProtKB:  P62861
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S27a
f
72Homo sapiensMutation(s): 0 
Gene Names: RPS27A
Find proteins for Q5RKT7 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  Q5RKT7
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Receptor of activated protein C kinase 1
g
315Homo sapiensMutation(s): 0 
Gene Names: RACK1 (GNB2L1)
Find proteins for P63244 (Homo sapiens)
Go to Gene View: RACK1
Go to UniProtKB:  P63244
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN EL41
h
24Homo sapiensMutation(s): 0 
Gene Names: RPL41
Find proteins for P62945 (Homo sapiens)
Go to Gene View: RPL41
Go to UniProtKB:  P62945
Entity ID: 2
MoleculeChainsLengthOrganism
initiator Met-tRNA-i175Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
18S ribosomal RNA21868Homo sapiens
Entity ID: 4
MoleculeChainsLengthOrganism
IRES mRNA3275Hepacivirus C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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