› 6zmw

Electron Microscopy
3.7Å resolution

Structure of a human 48S translational initiation complex

Released:
DOI: 10.2210/pdb6zmw/pdb
PDB entry 6zmw coloured by chain, front view.
PDB entry 6zmw coloured by chain, side view.
PDB entry 6zmw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of a human 48S translational initiation complex.
Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM, Fraser CS, Ramakrishnan V
Science 369 1220-1227 (2020)
PMID: 32883864
Related structures: EMD-11302

Function and Biology Details

Reactions catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
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
GTP + H(2)O = GDP + phosphate
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-126233 (preferred)
Entry contents:
54 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (57 distinct):
Eukaryotic translation initiation factor 3 subunit I Chain: 2
Molecule details ›
Chain: 2
Length: 325 amino acids
Theoretical weight: 36.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13347 (Residues: 1-325; Coverage: 100%)
Gene names: EIF3I, EIF3S2, TRIP1
Sequence domains:
Eukaryotic translation initiation factor 3 subunit B Chain: 1
Molecule details ›
Chain: 1
Length: 814 amino acids
Theoretical weight: 92.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55884 (Residues: 1-814; Coverage: 100%)
Gene names: EIF3B, EIF3S9
Sequence domains:
Eukaryotic translation initiation factor 3 subunit M Chain: 6
Molecule details ›
Chain: 6
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 F Chain: 4
Molecule details ›
Chain: 4
Length: 357 amino acids
Theoretical weight: 37.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00303 (Residues: 1-357; Coverage: 100%)
Gene names: EIF3F, EIF3S5
Sequence domains:
Eukaryotic translation initiation factor 3 subunit A Chain: u
Molecule details ›
Chain: u
Length: 1382 amino acids
Theoretical weight: 166.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14152 (Residues: 1-1382; Coverage: 100%)
Gene names: EIF3A, EIF3S10, KIAA0139
Sequence domains:
Eukaryotic translation initiation factor 3 subunit E Chain: v
Molecule details ›
Chain: v
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:
Small ribosomal subunit protein eS6 Chain: S
Molecule details ›
Chain: S
Length: 249 amino acids
Theoretical weight: 28.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62753 (Residues: 1-249; Coverage: 100%)
Gene names: OK/SW-cl.2, RPS6
Sequence domains: Ribosomal protein S6e
Eukaryotic translation initiation factor 3 subunit C Chain: y
Molecule details ›
Chain: y
Length: 913 amino acids
Theoretical weight: 105.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99613 (Residues: 1-913; Coverage: 100%)
Gene names: EIF3C, EIF3S8
Sequence domains:
Eukaryotic translation initiation factor 3 subunit H Chain: 8
Molecule details ›
Chain: 8
Length: 352 amino acids
Theoretical weight: 39.98 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15372 (Residues: 1-352; Coverage: 100%)
Gene names: EIF3H, EIF3S3
Sequence domains:
Small ribosomal subunit protein eS7 Chain: G
Molecule details ›
Chain: G
Length: 194 amino acids
Theoretical weight: 22.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 1-194; Coverage: 100%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS27 Chain: H
Molecule details ›
Chain: H
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 eS21 Chain: K
Molecule details ›
Chain: K
Length: 83 amino acids
Theoretical weight: 9.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63220 (Residues: 1-83; Coverage: 100%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS5 Chain: L
Molecule details ›
Chain: L
Length: 293 amino acids
Theoretical weight: 31.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P15880 (Residues: 1-293; Coverage: 100%)
Gene names: RPS2, RPS4
Sequence domains:
Small ribosomal subunit protein eS1 Chain: O
Molecule details ›
Chain: O
Length: 264 amino acids
Theoretical weight: 30 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61247 (Residues: 1-264; Coverage: 100%)
Gene names: FTE1, MFTL, RPS3A
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS2 Chain: N
Molecule details ›
Chain: N
Length: 295 amino acids
Theoretical weight: 32.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 1-295; Coverage: 100%)
Gene names: LAMBR, LAMR1, RPSA
Sequence domains:
Small ribosomal subunit protein eS26 Chain: Q
Molecule details ›
Chain: Q
Length: 115 amino acids
Theoretical weight: 13.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62854 (Residues: 1-115; Coverage: 100%)
Gene name: RPS26
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein uS11 Chain: P
Molecule details ›
Chain: P
Length: 151 amino acids
Theoretical weight: 16.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62263 (Residues: 1-151; Coverage: 100%)
Gene names: PRO2640, RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS15 Chain: I
Molecule details ›
Chain: I
Length: 151 amino acids
Theoretical weight: 17.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62277 (Residues: 1-151; Coverage: 100%)
Gene name: RPS13
Sequence domains:
Eukaryotic translation initiation factor 3 subunit D Chain: x
Molecule details ›
Chain: x
Length: 548 amino acids
Theoretical weight: 64.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15371 (Residues: 1-548; Coverage: 100%)
Gene names: EIF3D, EIF3S7
Sequence domains: Eukaryotic translation initiation factor 3 subunit 7 (eIF-3)
Eukaryotic translation initiation factor 3 subunit K Chain: 3
Molecule details ›
Chain: 3
Length: 218 amino acids
Theoretical weight: 25.08 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: 5
Molecule details ›
Chain: 5
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
Small ribosomal subunit protein eS32 Chain: 9
Molecule details ›
Chain: 9
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62945 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Sequence domains: Ribosomal protein L41
Small ribosomal subunit protein uS17 Chain: B
Molecule details ›
Chain: B
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 eS4, X isoform Chain: C
Molecule details ›
Chain: C
Length: 263 amino acids
Theoretical weight: 29.65 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 uS4 Chain: D
Molecule details ›
Chain: D
Length: 194 amino acids
Theoretical weight: 22.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46781 (Residues: 1-194; Coverage: 100%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein uS12 Chain: E
Molecule details ›
Chain: E
Length: 143 amino acids
Theoretical weight: 15.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62266 (Residues: 1-143; Coverage: 100%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS30 Chain: F
Molecule details ›
Chain: F
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62861 (Residues: 75-133; Coverage: 44%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Eukaryotic translation initiation factor 2 subunit 1 Chain: r
Molecule details ›
Chain: r
Length: 315 amino acids
Theoretical weight: 36.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P05198 (Residues: 1-315; Coverage: 100%)
Gene names: EIF2A, EIF2S1
Sequence domains:
Small ribosomal subunit protein uS8 Chain: J
Molecule details ›
Chain: J
Length: 130 amino acids
Theoretical weight: 14.87 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62244 (Residues: 1-130; Coverage: 100%)
Gene names: OK/SW-cl.82, RPS15A
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein eS8 Chain: R
Molecule details ›
Chain: R
Length: 208 amino acids
Theoretical weight: 24.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62241 (Residues: 1-208; Coverage: 100%)
Gene names: OK/SW-cl.83, RPS8
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein eS24 Chain: T
Molecule details ›
Chain: T
Length: 133 amino acids
Theoretical weight: 15.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62847 (Residues: 1-133; Coverage: 100%)
Gene name: RPS24
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein uS7 Chain: V
Molecule details ›
Chain: V
Length: 204 amino acids
Theoretical weight: 22.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46782 (Residues: 1-204; Coverage: 100%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS9 Chain: Y
Molecule details ›
Chain: Y
Length: 146 amino acids
Theoretical weight: 16.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 1-146; Coverage: 100%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS3 Chain: Z
Molecule details ›
Chain: Z
Length: 243 amino acids
Theoretical weight: 26.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P23396 (Residues: 1-243; Coverage: 100%)
Gene names: OK/SW-cl.26, RPS3
Sequence domains:
Small ribosomal subunit protein eS10 Chain: a
Molecule details ›
Chain: a
Length: 165 amino acids
Theoretical weight: 18.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46783 (Residues: 1-165; Coverage: 100%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein uS19 Chain: b
Molecule details ›
Chain: b
Length: 145 amino acids
Theoretical weight: 17.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 1-145; Coverage: 100%)
Gene names: RIG, RPS15
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein RACK1 Chain: c
Molecule details ›
Chain: c
Length: 317 amino acids
Theoretical weight: 35.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63244 (Residues: 1-317; Coverage: 100%)
Gene names: GNB2L1, HLC7, PIG21, RACK1
Sequence domains: WD domain, G-beta repeat
Small ribosomal subunit protein eS19 Chain: d
Molecule details ›
Chain: d
Length: 145 amino acids
Theoretical weight: 16.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39019 (Residues: 1-145; Coverage: 100%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein eS25 Chain: e
Molecule details ›
Chain: e
Length: 125 amino acids
Theoretical weight: 13.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62851 (Residues: 1-125; Coverage: 100%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein uS13 Chain: f
Molecule details ›
Chain: f
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 1-152; Coverage: 100%)
Gene names: D6S218E, RPS18
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: i
Molecule details ›
Chain: i
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Ubiquitin-ribosomal protein eS31 fusion protein Chain: k
Molecule details ›
Chain: k
Length: 156 amino acids
Theoretical weight: 18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62979 (Residues: 1-156; Coverage: 100%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains:
Small ribosomal subunit protein eS12 Chain: m
Molecule details ›
Chain: m
Length: 132 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 1-132; Coverage: 100%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein eS28 Chain: n
Molecule details ›
Chain: n
Length: 69 amino acids
Theoretical weight: 7.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62857 (Residues: 1-69; Coverage: 100%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Eukaryotic translation initiation factor 3 subunit G Chain: o
Molecule details ›
Chain: o
Length: 320 amino acids
Theoretical weight: 35.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75821 (Residues: 1-320; Coverage: 100%)
Gene names: EIF3G, EIF3S4
Sequence domains:
Eukaryotic translation initiation factor 1 Chain: p
Molecule details ›
Chain: p
Length: 113 amino acids
Theoretical weight: 12.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P41567 (Residues: 1-113; Coverage: 100%)
Gene names: EIF1, SUI1
Sequence domains: Translation initiation factor SUI1
Eukaryotic translation initiation factor 1A, X-chromosomal Chain: q
Molecule details ›
Chain: q
Length: 144 amino acids
Theoretical weight: 16.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P47813 (Residues: 1-144; Coverage: 100%)
Gene names: EIF1A, EIF1AX, EIF4C
Sequence domains: Translation initiation factor 1A / IF-1
Eukaryotic translation initiation factor 3 subunit J Chain: z
Molecule details ›
Chain: z
Length: 258 amino acids
Theoretical weight: 29.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75822 (Residues: 1-258; Coverage: 100%)
Gene names: EIF3J, EIF3S1, PRO0391
Sequence domains: Translation initiation factor eIF3 subunit
Small ribosomal subunit protein eS17 Chain: M
Molecule details ›
Chain: M
Length: 135 amino acids
Theoretical weight: 15.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08708 (Residues: 1-135; Coverage: 100%)
Gene names: RPS17, RPS17L
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS10 Chain: h
Molecule details ›
Chain: h
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60866 (Residues: 1-119; Coverage: 100%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Eukaryotic translation initiation factor 2 subunit 2 Chain: s
Molecule details ›
Chain: s
Length: 333 amino acids
Theoretical weight: 38.45 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P20042 (Residues: 1-333; Coverage: 100%)
Gene names: EIF2B, EIF2S2
Sequence domains: Domain found in IF2B/IF5
Eukaryotic translation initiation factor 2 subunit 3 Chain: t
Molecule details ›
Chain: t
Length: 472 amino acids
Theoretical weight: 51.18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P41091 (Residues: 1-472; Coverage: 100%)
Gene names: EIF2G, EIF2S3
Sequence domains:
Eukaryotic initiation factor 4A-I Chain: j
Molecule details ›
Chain: j
Length: 406 amino acids
Theoretical weight: 46.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P60842 (Residues: 1-406; Coverage: 100%)
Gene names: DDX2A, EIF4A, EIF4A1
Sequence domains:
Eukaryotic translation initiation factor 4 gamma 1 Chain: g
Molecule details ›
Chain: g
Length: 1310 amino acids
Theoretical weight: 145.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q04637 (Residues: 290-1599; Coverage: 82%)
  • Best match: Q04637-7 (Residues: 94-1404)
Gene names: EIF4F, EIF4G, EIF4G1, EIF4GI
Sequence domains:
Messenger RNA Chain: 7
Molecule details ›
Chain: 7
Length: 28 nucleotides
Theoretical weight: 9.17 KDa
18S Ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1869 nucleotides
Theoretical weight: 603.13 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
Initiator Met-tRNA-i Chain: w
Molecule details ›
Chain: w
Length: 75 nucleotides
Theoretical weight: 24.23 KDa
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 89 x MG
11 modified residues:
Ligand A2M 7 x A2M
Ligand OMU 2 x OMU
Ligand PSU 6 x PSU
Ligand OMC 3 x OMC
Ligand OMG 3 x OMG
Ligand 5MU 1 x 5MU
Ligand JMH 1 x JMH
Ligand 5MC 1 x 5MC
Ligand UR3 1 x UR3
Ligand 6MZ 1 x 6MZ
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-11302
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Control of the eIF4E activity: structural insights and pharmacological implications.
Romagnoli et al. (2021)
11 more

12 mentions without citation

Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation.
Lapointe et al. (2021)
11 more