› 6zvj

Electron Microscopy
3.8Å resolution

Structure of a human ABCE1-bound 43S pre-initiation complex - State II

Released:
DOI: 10.2210/pdb6zvj/pdb
PDB entry 6zvj coloured by chain, front view.
PDB entry 6zvj coloured by chain, side view.
PDB entry 6zvj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes.
Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R
EMBO J 40 e105179 (2021)
PMID: 33289941
Related structures: EMD-11458

Function and Biology Details

Reactions catalysed: 
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
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).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 51-mer (preferred)
PDBe Complex ID:
PDB-CPX-104449 (preferred)
Entry contents:
49 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (50 distinct):
Small ribosomal subunit protein uS2 Chain: a
Molecule details ›
Chain: a
Length: 216 amino acids
Theoretical weight: 24.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 2-217; Coverage: 73%)
Gene names: LAMBR, LAMR1, RPSA
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1 Chain: p
Molecule details ›
Chain: p
Length: 211 amino acids
Theoretical weight: 24.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61247 (Residues: 23-233; Coverage: 80%)
Gene names: FTE1, MFTL, RPS3A
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS5 Chain: d
Molecule details ›
Chain: d
Length: 216 amino acids
Theoretical weight: 23.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P15880 (Residues: 60-275; Coverage: 74%)
Gene names: RPS2, RPS4
Sequence domains:
Small ribosomal subunit protein eS26 Chain: Q
Molecule details ›
Chain: Q
Length: 101 amino acids
Theoretical weight: 11.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62854 (Residues: 2-102; Coverage: 88%)
Gene name: RPS26
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein eS4, X isoform Chain: q
Molecule details ›
Chain: q
Length: 255 amino acids
Theoretical weight: 28.89 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62701 (Residues: 2-256; Coverage: 97%)
Gene names: CCG2, RPS4, RPS4X, SCAR
Sequence domains:
Small ribosomal subunit protein eS32 Chain: W
Molecule details ›
Chain: W
Length: 24 amino acids
Theoretical weight: 3.34 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62945 (Residues: 1-24; Coverage: 96%)
Gene name: RPL41
Sequence domains: Ribosomal protein L41
Small ribosomal subunit protein eS6 Chain: r
Molecule details ›
Chain: r
Length: 222 amino acids
Theoretical weight: 25.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62753 (Residues: 2-223; Coverage: 89%)
Gene names: OK/SW-cl.2, RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7 Chain: s
Molecule details ›
Chain: s
Length: 181 amino acids
Theoretical weight: 20.79 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 13-193; Coverage: 93%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8 Chain: t
Molecule details ›
Chain: t
Length: 205 amino acids
Theoretical weight: 23.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62241 (Residues: 2-206; Coverage: 99%)
Gene names: OK/SW-cl.83, RPS8
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4 Chain: c
Molecule details ›
Chain: c
Length: 180 amino acids
Theoretical weight: 21.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46781 (Residues: 2-181; Coverage: 93%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein uS17 Chain: n
Molecule details ›
Chain: n
Length: 144 amino acids
Theoretical weight: 16.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62280 (Residues: 4-147; Coverage: 91%)
Gene name: RPS11
Sequence domains:
Small ribosomal subunit protein uS15 Chain: m
Molecule details ›
Chain: m
Length: 149 amino acids
Theoretical weight: 17.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62277 (Residues: 2-150; Coverage: 99%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein uS11 Chain: i
Molecule details ›
Chain: i
Length: 125 amino acids
Theoretical weight: 13.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: A0A2R8Y811 (Residues: 26-150; Coverage: 83%)
Gene name: RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein eS21 Chain: y
Molecule details ›
Chain: y
Length: 82 amino acids
Theoretical weight: 8.98 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63220 (Residues: 1-82; Coverage: 99%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS8 Chain: f
Molecule details ›
Chain: f
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
Small ribosomal subunit protein uS12 Chain: j
Molecule details ›
Chain: j
Length: 139 amino acids
Theoretical weight: 15.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62266 (Residues: 2-140; Coverage: 97%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S24 Chain: z
Molecule details ›
Chain: z
Length: 122 amino acids
Theoretical weight: 14.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: E7ETK0 (Residues: 5-126; Coverage: 93%)
Gene name: RPS24
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS27 Chain: R
Molecule details ›
Chain: R
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42677 (Residues: 2-83; Coverage: 98%)
Gene names: MPS1, RPS27
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS30 Chain: T
Molecule details ›
Chain: T
Length: 44 amino acids
Theoretical weight: 5.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62861 (Residues: 81-124; Coverage: 33%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein eS17 Chain: w
Molecule details ›
Chain: w
Length: 130 amino acids
Theoretical weight: 15.04 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08708 (Residues: 2-131; Coverage: 96%)
Gene names: RPS17, RPS17L
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS9 Chain: g
Molecule details ›
Chain: g
Length: 138 amino acids
Theoretical weight: 15.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 9-146; Coverage: 95%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS3 Chain: b
Molecule details ›
Chain: b
Length: 224 amino acids
Theoretical weight: 24.87 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P23396 (Residues: 4-227; Coverage: 92%)
Gene names: OK/SW-cl.26, RPS3
Sequence domains:
Small ribosomal subunit protein uS7 Chain: e
Molecule details ›
Chain: e
Length: 189 amino acids
Theoretical weight: 21.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46782 (Residues: 16-204; Coverage: 93%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS10 Chain: u
Molecule details ›
Chain: u
Length: 95 amino acids
Theoretical weight: 11.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46783 (Residues: 1-95; Coverage: 58%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein eS12 Chain: v
Molecule details ›
Chain: v
Length: 116 amino acids
Theoretical weight: 12.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 14-129; Coverage: 88%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS19 Chain: o
Molecule details ›
Chain: o
Length: 119 amino acids
Theoretical weight: 14.01 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 15-133; Coverage: 82%)
Gene names: RIG, RPS15
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS13 Chain: k
Molecule details ›
Chain: k
Length: 140 amino acids
Theoretical weight: 16.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 3-142; Coverage: 92%)
Gene names: D6S218E, RPS18
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein eS19 Chain: x
Molecule details ›
Chain: x
Length: 141 amino acids
Theoretical weight: 15.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39019 (Residues: 2-142; Coverage: 97%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chain: h
Molecule details ›
Chain: h
Length: 98 amino acids
Theoretical weight: 11.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60866 (Residues: 19-116; Coverage: 82%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein eS25 Chain: P
Molecule details ›
Chain: P
Length: 70 amino acids
Theoretical weight: 7.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62851 (Residues: 44-113; Coverage: 56%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS28 Chain: S
Molecule details ›
Chain: S
Length: 61 amino acids
Theoretical weight: 6.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62857 (Residues: 8-68; Coverage: 88%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14 Chain: l
Molecule details ›
Chain: l
Length: 54 amino acids
Theoretical weight: 6.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 2-55; Coverage: 96%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS31 Chain: U
Molecule details ›
Chain: U
Length: 62 amino acids
Theoretical weight: 7.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62979 (Residues: 88-149; Coverage: 40%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein RACK1 Chain: V
Molecule details ›
Chain: V
Length: 309 amino acids
Theoretical weight: 34.22 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63244 (Residues: 4-312; Coverage: 98%)
Gene names: GNB2L1, HLC7, PIG21, RACK1
Sequence domains: WD domain, G-beta repeat
Eukaryotic translation initiation factor 3 subunit I Chain: I
Molecule details ›
Chain: I
Length: 316 amino acids
Theoretical weight: 35.35 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13347 (Residues: 1-316; Coverage: 97%)
Gene names: EIF3I, EIF3S2, TRIP1
Sequence domains:
Eukaryotic translation initiation factor 3 subunit B Chain: B
Molecule details ›
Chain: B
Length: 566 amino acids
Theoretical weight: 65.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55884 (Residues: 180-745; Coverage: 70%)
Gene names: EIF3B, EIF3S9
Sequence domains:
Eukaryotic translation initiation factor 3 subunit A Chain: A
Molecule details ›
Chain: A
Length: 722 amino acids
Theoretical weight: 85.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14152 (Residues: 4-725; Coverage: 52%)
Gene names: EIF3A, EIF3S10, KIAA0139
Sequence domains: PCI domain
Eukaryotic translation initiation factor 3 subunit C Chain: C
Molecule details ›
Chain: C
Length: 743 amino acids
Theoretical weight: 86.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: B4DVU3 (Residues: 1-129, 130-761; Coverage: 98%)
Gene names: EIF3C, EIF3S8
Sequence domains:
Eukaryotic translation initiation factor 3 subunit E Chain: E
Molecule details ›
Chain: E
Length: 429 amino acids
Theoretical weight: 50.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60228 (Residues: 2-430; Coverage: 96%)
Gene names: EIF3E, EIF3S6, INT6
Sequence domains:
Eukaryotic translation initiation factor 3 subunit F Chain: F
Molecule details ›
Chain: F
Length: 269 amino acids
Theoretical weight: 29.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00303 (Residues: 89-357; Coverage: 75%)
Gene names: EIF3F, EIF3S5
Sequence domains:
Eukaryotic translation initiation factor 3 subunit H Chain: H
Molecule details ›
Chain: H
Length: 318 amino acids
Theoretical weight: 36.96 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15372 (Residues: 35-352; Coverage: 90%)
Gene names: EIF3H, EIF3S3
Sequence domains:
Eukaryotic translation initiation factor 3 subunit K Chain: K
Molecule details ›
Chain: K
Length: 217 amino acids
Theoretical weight: 24.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UBQ5 (Residues: 2-218; Coverage: 100%)
Gene names: ARG134, EIF3K, EIF3S12, HSPC029, MSTP001, PTD001
Sequence domains: CSN8/PSMD8/EIF3K family
Eukaryotic translation initiation factor 3 subunit L Chain: L
Molecule details ›
Chain: L
Length: 372 amino acids
Theoretical weight: 44.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y262 (Residues: 181-552; Coverage: 66%)
Gene names: EIF3EIP, EIF3L, EIF3S6IP, HSPC021, HSPC025, MSTP005
Sequence domains: RNA polymerase I-associated factor PAF67
Eukaryotic translation initiation factor 3 subunit M Chain: M
Molecule details ›
Chain: M
Length: 362 amino acids
Theoretical weight: 41.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7L2H7 (Residues: 11-372; Coverage: 97%)
Gene names: EIF3M, GA17, HFLB5, PCID1, PNAS-125
Sequence domains:
ATP-binding cassette sub-family E member 1 Chain: 1
Molecule details ›
Chain: 1
Length: 595 amino acids
Theoretical weight: 66.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61221 (Residues: 4-598; Coverage: 99%)
Gene names: ABCE1, OK/SW-cl.40, RLI, RNASEL1, RNASELI, RNS4I
Sequence domains:
Eukaryotic translation initiation factor 1 Chain: N
Molecule details ›
Chain: N
Length: 91 amino acids
Theoretical weight: 10.39 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P41567 (Residues: 23-113; Coverage: 81%)
Gene names: EIF1, SUI1
Sequence domains: Translation initiation factor SUI1
Eukaryotic translation initiation factor 3 subunit D Chain: D
Molecule details ›
Chain: D
Length: 527 amino acids
Theoretical weight: 61.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15371 (Residues: 1-527; Coverage: 96%)
Gene names: EIF3D, EIF3S7
Sequence domains: Eukaryotic translation initiation factor 3 subunit 7 (eIF-3)
RNA recognition motif (unknown) Chain: Y
Molecule details ›
Chain: Y
Length: 78 amino acids
Theoretical weight: 5.56 KDa
Source organism: Homo sapiens
Eukaryotic translation initiation factor 3 subunit J Chains: G, J
Molecule details ›
Chains: G, J
Length: 258 amino acids
Theoretical weight: 29.11 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75822 (Residues: 1-258; Coverage: 100%)
Gene names: EIF3J, EIF3S1, PRO0391
Sequence domains: Translation initiation factor eIF3 subunit
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1720 nucleotides
Theoretical weight: 555.21 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

5 bound ligands:
Ligand ZN 3 x ZN
Ligand SF4 2 x SF4
Ligand ADP 1 x ADP
Ligand MG 2 x MG
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-11458

Quick links

Citations

5 review citations

Iron-sulfur clusters as inhibitors and catalysts of viral replication.
Honarmand Ebrahimi et al. (2022)
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