6FEC

Human cap-dependent 48S pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.3 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

Structure of a human cap-dependent 48S translation pre-initiation complex.

Eliseev, B.Yeramala, L.Leitner, A.Karuppasamy, M.Raimondeau, E.Huard, K.Alkalaeva, E.Aebersold, R.Schaffitzel, C.

(2018) Nucleic Acids Res. 46: 2678-2689

  • DOI: 10.1093/nar/gky054

  • PubMed Abstract: 
  • Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprisi ...

    Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit A
1
1362N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit C
2
843N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit E
3
445Homo sapiensMutation(s): 0 
Gene Names: EIF3E (EIF3S6, INT6)
Find proteins for P60228 (Homo sapiens)
Go to Gene View: EIF3E
Go to UniProtKB:  P60228
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit F
4
364N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit H
5
352N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit K
6
218Homo sapiensMutation(s): 0 
Gene Names: EIF3K (EIF3S12)
Find proteins for Q9UBQ5 (Homo sapiens)
Go to Gene View: EIF3K
Go to UniProtKB:  Q9UBQ5
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit L
7
564Homo sapiensMutation(s): 0 
Gene Names: EIF3L (EIF3EIP, EIF3S6IP)
Find proteins for Q9Y262 (Homo sapiens)
Go to Gene View: EIF3L
Go to UniProtKB:  Q9Y262
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit M
8
374Homo sapiensMutation(s): 0 
Gene Names: EIF3M (HFLB5, PCID1)
Find proteins for Q7L2H7 (Homo sapiens)
Go to Gene View: EIF3M
Go to UniProtKB:  Q7L2H7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D
9
368N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
G
158Homo sapiensMutation(s): 0 
Gene Names: RPS11
Find proteins for P62280 (Homo sapiens)
Go to Gene View: RPS11
Go to UniProtKB:  P62280
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
H
141Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
Go to Gene View: RPS16
Go to UniProtKB:  P62249
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4, X isoform
I
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: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29
J
53Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
Go to Gene View: RPS29
Go to UniProtKB:  P62273
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9
K
182Homo sapiensMutation(s): 0 
Gene Names: RPS9
Find proteins for P46781 (Homo sapiens)
Go to Gene View: RPS9
Go to UniProtKB:  P46781
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
L
137Homo sapiensMutation(s): 0 
Gene Names: RPS18 (D6S218E)
Find proteins for P62269 (Homo sapiens)
Go to Gene View: RPS18
Go to UniProtKB:  P62269
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2 subunit 1
P
266N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
Q
142Homo sapiensMutation(s): 0 
Gene Names: RPS23
Find proteins for P62266 (Homo sapiens)
Go to Gene View: RPS23
Go to UniProtKB:  P62266
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
R
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2 subunit 3
S
422Homo sapiensMutation(s): 0 
Gene Names: EIF2S3 (EIF2G)
Find proteins for P41091 (Homo sapiens)
Go to Gene View: EIF2S3
Go to UniProtKB:  P41091
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
U
191Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
Go to Gene View: RPS5
Go to UniProtKB:  P46782
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
V
59Homo sapiensMutation(s): 0 
Gene Names: FAU
Find proteins for P62861 (Homo sapiens)
Go to Gene View: FAU
Go to UniProtKB:  P62861
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25
W
75Homo sapiensMutation(s): 0 
Gene Names: RPS25
Find proteins for P62851 (Homo sapiens)
Go to Gene View: RPS25
Go to UniProtKB:  P62851
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
X
190Homo sapiensMutation(s): 0 
Gene Names: RPS7
Find proteins for P62081 (Homo sapiens)
Go to Gene View: RPS7
Go to UniProtKB:  P62081
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
Y
84Homo sapiensMutation(s): 0 
Gene Names: RPS27 (MPS1)
Find proteins for P42677 (Homo sapiens)
Go to Gene View: RPS27
Go to UniProtKB:  P42677
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
Z
150Homo sapiensMutation(s): 0 
Gene Names: RPS13
Find proteins for P62277 (Homo sapiens)
Go to Gene View: RPS13
Go to UniProtKB:  P62277
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15a
a
129Homo sapiensMutation(s): 0 
Gene Names: RPS15A
Find proteins for P62244 (Homo sapiens)
Go to Gene View: RPS15A
Go to UniProtKB:  P62244
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
b
82N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
c
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)
d
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17
e
126Homo sapiensMutation(s): 0 
Gene Names: RPS17 (RPS17L)
Find proteins for P08708 (Homo sapiens)
Go to Gene View: RPS17
Go to UniProtKB:  P08708
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
f
208Homo 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: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
g
227Homo 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: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
h
104Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
Go to Gene View: RPS20
Go to UniProtKB:  P60866
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
i
215Homo 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: 38
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
j
136Homo sapiensMutation(s): 0 
Gene Names: RPS14
Find proteins for P62263 (Homo sapiens)
Go to Gene View: RPS14
Go to UniProtKB:  P62263
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26
k
99N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28
l
64Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
Go to Gene View: RPS28
Go to UniProtKB:  P62857
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Receptor of activated protein C kinase 1
m
313Homo sapiensMutation(s): 0 
Gene Names: RACK1 (GNB2L1)
Find proteins for P63244 (Homo sapiens)
Go to Gene View: RACK1
Go to UniProtKB:  P63244
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
n
127Homo sapiensMutation(s): 0 
Gene Names: RPS15 (RIG)
Find proteins for P62841 (Homo sapiens)
Go to Gene View: RPS15
Go to UniProtKB:  P62841
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
o
206Homo sapiensMutation(s): 0 
Gene Names: RPS8
Find proteins for P62241 (Homo sapiens)
Go to Gene View: RPS8
Go to UniProtKB:  P62241
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27a
p
71Homo sapiensMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
q
237Homo sapiensMutation(s): 0 
Gene Names: RPS6
Find proteins for P62753 (Homo sapiens)
Go to Gene View: RPS6
Go to UniProtKB:  P62753
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
r
124Homo sapiensMutation(s): 0 
Gene Names: RPS12
Find proteins for P25398 (Homo sapiens)
Go to Gene View: RPS12
Go to UniProtKB:  P25398
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
s
131Homo sapiensMutation(s): 0 
Gene Names: RPS24
Find proteins for P62847 (Homo sapiens)
Go to Gene View: RPS24
Go to UniProtKB:  P62847
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10
t
98Homo sapiensMutation(s): 0 
Gene Names: RPS10
Find proteins for P46783 (Homo sapiens)
Go to Gene View: RPS10
Go to UniProtKB:  P46783
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 4B
u
636Homo sapiensMutation(s): 0 
Gene Names: EIF4B
Find proteins for P23588 (Homo sapiens)
Go to Gene View: EIF4B
Go to UniProtKB:  P23588
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit B
w
1121N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsLengthOrganism
18S ribosomal RNAA1776Homo sapiens
Entity ID: 11
MoleculeChainsLengthOrganism
Messenger RNA (26-MER)F26Homo sapiens
Entity ID: 18
MoleculeChainsLengthOrganism
Transfer RNA (75-MER)N75Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium281331
EMBL-RFBRBelgium15-54-74001

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Refinement description