› 6fec

Electron Microscopy
6.3Å resolution

Human cap-dependent 48S pre-initiation complex

Released:
DOI: 10.2210/pdb6fec/pdb
PDB entry 6fec coloured by chain, front view.
PDB entry 6fec coloured by chain, side view.
PDB entry 6fec coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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
Nucleic Acids Res 46 2678-2689 (2018)
PMID: 29401259
Related structures: EMD-4242

Function and Biology Details

Reactions catalysed: 
GTP + H(2)O = GDP + phosphate
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 50-mer (preferred)
PDBe Complex ID:
PDB-CPX-140348 (preferred)
Entry contents:
47 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (50 distinct):
Eukaryotic translation initiation factor 3 subunit A Chain: 1
Molecule details ›
Chain: 1
Length: 1362 amino acids
Theoretical weight: 164.9 KDa
Source organism: Homo sapiens
Eukaryotic translation initiation factor 3 subunit C Chain: 2
Molecule details ›
Chain: 2
Length: 843 amino acids
Theoretical weight: 97.92 KDa
Source organism: Homo sapiens
Eukaryotic translation initiation factor 3 subunit E Chain: 3
Molecule details ›
Chain: 3
Length: 445 amino acids
Theoretical weight: 52.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60228 (Residues: 1-445; Coverage: 100%)
Gene names: EIF3E, EIF3S6, INT6
Sequence domains:
Eukaryotic translation initiation factor 3 subunit F Chain: 4
Molecule details ›
Chain: 4
Length: 364 amino acids
Theoretical weight: 37.85 KDa
Source organism: Homo sapiens
Eukaryotic translation initiation factor 3 subunit H Chain: 5
Molecule details ›
Chain: 5
Length: 352 amino acids
Theoretical weight: 39.95 KDa
Source organism: Homo sapiens
Eukaryotic translation initiation factor 3 subunit K Chain: 6
Molecule details ›
Chain: 6
Length: 218 amino acids
Theoretical weight: 25.13 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UBQ5 (Residues: 1-218; Coverage: 100%)
Gene names: ARG134, EIF3K, EIF3S12, HSPC029, MSTP001, PTD001
Sequence domains: CSN8/PSMD8/EIF3K family
Eukaryotic translation initiation factor 3 subunit L Chain: 7
Molecule details ›
Chain: 7
Length: 564 amino acids
Theoretical weight: 66.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y262 (Residues: 1-564; Coverage: 100%)
Gene names: EIF3EIP, EIF3L, EIF3S6IP, HSPC021, HSPC025, MSTP005
Sequence domains: RNA polymerase I-associated factor PAF67
Eukaryotic translation initiation factor 3 subunit M Chain: 8
Molecule details ›
Chain: 8
Length: 374 amino acids
Theoretical weight: 42.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7L2H7 (Residues: 1-374; Coverage: 100%)
Gene names: EIF3M, GA17, HFLB5, PCID1, PNAS-125
Sequence domains:
EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D Chain: 9
Molecule details ›
Chain: 9
Length: 368 amino acids
Theoretical weight: 42.2 KDa
Source organism: Homo sapiens
Small ribosomal subunit protein uS17 Chain: G
Molecule details ›
Chain: G
Length: 158 amino acids
Theoretical weight: 18.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62280 (Residues: 1-158; Coverage: 100%)
Gene name: RPS11
Sequence domains:
Small ribosomal subunit protein uS9 Chain: H
Molecule details ›
Chain: H
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 6-146; Coverage: 97%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS4, X isoform Chain: I
Molecule details ›
Chain: I
Length: 263 amino acids
Theoretical weight: 29.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62701 (Residues: 1-263; Coverage: 100%)
Gene names: CCG2, RPS4, RPS4X, SCAR
Sequence domains:
Small ribosomal subunit protein uS14 Chain: J
Molecule details ›
Chain: J
Length: 53 amino acids
Theoretical weight: 6.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 4-56; Coverage: 95%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS4 Chain: K
Molecule details ›
Chain: K
Length: 182 amino acids
Theoretical weight: 21.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46781 (Residues: 7-188; Coverage: 94%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein uS13 Chain: L
Molecule details ›
Chain: L
Length: 137 amino acids
Theoretical weight: 16.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 6-142; Coverage: 90%)
Gene names: D6S218E, RPS18
Sequence domains: Ribosomal protein S13/S18
Eukaryotic translation initiation factor 2 subunit 1 Chain: P
Molecule details ›
Chain: P
Length: 266 amino acids
Theoretical weight: 30.63 KDa
Source organism: Homo sapiens
Small ribosomal subunit protein uS12 Chain: Q
Molecule details ›
Chain: Q
Length: 142 amino acids
Theoretical weight: 15.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62266 (Residues: 1-142; Coverage: 99%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S19 Chain: R
Molecule details ›
Chain: R
Length: 141 amino acids
Theoretical weight: 15.81 KDa
Source organism: Homo sapiens
Eukaryotic translation initiation factor 2 subunit 3 Chain: S
Molecule details ›
Chain: S
Length: 422 amino acids
Theoretical weight: 45.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P41091 (Residues: 39-460; Coverage: 89%)
Gene names: EIF2G, EIF2S3
Sequence domains:
Small ribosomal subunit protein uS7 Chain: U
Molecule details ›
Chain: U
Length: 191 amino acids
Theoretical weight: 21.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46782 (Residues: 14-204; Coverage: 94%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS30 Chain: V
Molecule details ›
Chain: V
Length: 59 amino acids
Theoretical weight: 6.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62861 (Residues: 75-133; Coverage: 44%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein eS25 Chain: W
Molecule details ›
Chain: W
Length: 75 amino acids
Theoretical weight: 8.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62851 (Residues: 41-115; Coverage: 60%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS7 Chain: X
Molecule details ›
Chain: X
Length: 190 amino acids
Theoretical weight: 21.72 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 5-194; Coverage: 98%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS27 Chain: Y
Molecule details ›
Chain: Y
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42677 (Residues: 1-84; Coverage: 100%)
Gene names: MPS1, RPS27
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein uS15 Chain: Z
Molecule details ›
Chain: Z
Length: 150 amino acids
Theoretical weight: 17.13 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62277 (Residues: 2-151; Coverage: 99%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein uS8 Chain: a
Molecule details ›
Chain: a
Length: 129 amino acids
Theoretical weight: 14.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62244 (Residues: 2-130; Coverage: 99%)
Gene names: OK/SW-cl.82, RPS15A
Sequence domains: Ribosomal protein S8
40S ribosomal protein S21 Chain: b
Molecule details ›
Chain: b
Length: 82 amino acids
Theoretical weight: 8.9 KDa
Source organism: Homo sapiens
40S ribosomal protein S2 Chain: c
Molecule details ›
Chain: c
Length: 226 amino acids
Theoretical weight: 24.81 KDa
Source organism: Homo sapiens
EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta) Chain: d
Molecule details ›
Chain: d
Length: 17 amino acids
Theoretical weight: 2.1 KDa
Source organism: Homo sapiens
Small ribosomal subunit protein eS17 Chain: e
Molecule details ›
Chain: e
Length: 126 amino acids
Theoretical weight: 14.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08708 (Residues: 1-126; Coverage: 93%)
Gene names: RPS17, RPS17L
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS2 Chain: f
Molecule details ›
Chain: f
Length: 208 amino acids
Theoretical weight: 23.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 2-209; Coverage: 71%)
Gene names: LAMBR, LAMR1, RPSA
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: g
Molecule details ›
Chain: g
Length: 227 amino acids
Theoretical weight: 25.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P23396 (Residues: 1-227; Coverage: 93%)
Gene names: OK/SW-cl.26, RPS3
Sequence domains:
Small ribosomal subunit protein uS10 Chain: h
Molecule details ›
Chain: h
Length: 104 amino acids
Theoretical weight: 11.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60866 (Residues: 16-119; Coverage: 87%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein eS1 Chain: i
Molecule details ›
Chain: i
Length: 215 amino acids
Theoretical weight: 24.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61247 (Residues: 19-233; Coverage: 81%)
Gene names: FTE1, MFTL, RPS3A
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS11 Chain: j
Molecule details ›
Chain: j
Length: 136 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62263 (Residues: 16-151; Coverage: 90%)
Gene names: PRO2640, RPS14
Sequence domains: Ribosomal protein S11
40S ribosomal protein S26 Chain: k
Molecule details ›
Chain: k
Length: 99 amino acids
Theoretical weight: 11.32 KDa
Source organism: Homo sapiens
Small ribosomal subunit protein eS28 Chain: l
Molecule details ›
Chain: l
Length: 64 amino acids
Theoretical weight: 7.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62857 (Residues: 5-68; Coverage: 93%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein RACK1 Chain: m
Molecule details ›
Chain: m
Length: 313 amino acids
Theoretical weight: 34.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63244 (Residues: 2-314; Coverage: 99%)
Gene names: GNB2L1, HLC7, PIG21, RACK1
Sequence domains: WD domain, G-beta repeat
Small ribosomal subunit protein uS19 Chain: n
Molecule details ›
Chain: n
Length: 127 amino acids
Theoretical weight: 15.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 4-130; Coverage: 88%)
Gene names: RIG, RPS15
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein eS8 Chain: o
Molecule details ›
Chain: o
Length: 206 amino acids
Theoretical weight: 23.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62241 (Residues: 2-207; Coverage: 99%)
Gene names: OK/SW-cl.83, RPS8
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein eS31 Chain: p
Molecule details ›
Chain: p
Length: 71 amino acids
Theoretical weight: 8.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62979 (Residues: 82-152; Coverage: 46%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein eS6 Chain: q
Molecule details ›
Chain: q
Length: 237 amino acids
Theoretical weight: 27.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62753 (Residues: 1-237; Coverage: 95%)
Gene names: OK/SW-cl.2, RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS12 Chain: r
Molecule details ›
Chain: r
Length: 124 amino acids
Theoretical weight: 13.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 9-132; Coverage: 94%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein eS24 Chain: s
Molecule details ›
Chain: s
Length: 131 amino acids
Theoretical weight: 15.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62847 (Residues: 3-133; Coverage: 99%)
Gene name: RPS24
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS10 Chain: t
Molecule details ›
Chain: t
Length: 98 amino acids
Theoretical weight: 11.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46783 (Residues: 1-98; Coverage: 59%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
Eukaryotic translation initiation factor 4B Chain: u
Molecule details ›
Chain: u
Length: 636 amino acids
Theoretical weight: 72.32 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P23588 (Residues: 1-611; Coverage: 100%)
Gene name: EIF4B
Sequence domains: RNA recognition motif
Eukaryotic translation initiation factor 3 subunit B Chain: w
Molecule details ›
Chain: w
Length: 1121 amino acids
Theoretical weight: 124.4 KDa
Source organism: Homo sapiens
18S Ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1776 nucleotides
Theoretical weight: 572.79 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
Messenger RNA (26-MER) Chain: F
Molecule details ›
Chain: F
Length: 26 nucleotides
Theoretical weight: 8.24 KDa
Transfer RNA (75-MER) Chain: N
Molecule details ›
Chain: N
Length: 75 nucleotides
Theoretical weight: 24.23 KDa
Sequence domains: tRNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.3Å
Relevant EMDB volumes: EMD-4242
Expression system: Spodoptera frugiperda

Quick links

Citations

10 review citations

The Organizing Principles of Eukaryotic Ribosome Recruitment.
Pelletier et al. (2019)
9 more

8 mentions without citation

Structure of a human cap-dependent 48S translation pre-initiation complex.
Eliseev et al. (2018)
7 more