› 6zvh

Electron Microscopy
2.9Å resolution

EDF1-ribosome complex

Released:
DOI: 10.2210/pdb6zvh/pdb
PDB entry 6zvh coloured by chain, front view.
PDB entry 6zvh coloured by chain, side view.
PDB entry 6zvh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
EDF1 coordinates cellular responses to ribosome collisions.
Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M, Paulo JA, Harper JW, Bennett EJ, Beckmann R, Green R
Elife 9 (2020)
PMID: 32744497
Related structures: EMD-11456

Function and Biology Details

Reaction 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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 37-mer (preferred)
PDBe Complex ID:
PDB-CPX-130104 (preferred)
Entry contents:
35 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (37 distinct):
Small ribosomal subunit protein uS2 Chain: A
Molecule details ›
Chain: A
Length: 221 amino acids
Theoretical weight: 24.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 3-223; Coverage: 75%)
Gene names: LAMBR, LAMR1, RPSA
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1 Chain: B
Molecule details ›
Chain: B
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 uS3 Chain: D
Molecule details ›
Chain: D
Length: 227 amino acids
Theoretical weight: 25.17 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 eS4, X isoform Chain: E
Molecule details ›
Chain: E
Length: 262 amino acids
Theoretical weight: 29.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62701 (Residues: 2-263; Coverage: 100%)
Gene names: CCG2, RPS4, RPS4X, SCAR
Sequence domains:
Small ribosomal subunit protein uS7 Chain: F
Molecule details ›
Chain: F
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 eS7 Chain: H
Molecule details ›
Chain: H
Length: 189 amino acids
Theoretical weight: 21.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 5-193; Coverage: 97%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8 Chain: I
Molecule details ›
Chain: I
Length: 206 amino acids
Theoretical weight: 24 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 eS10 Chain: K
Molecule details ›
Chain: K
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
Small ribosomal subunit protein uS17 Chain: L
Molecule details ›
Chain: L
Length: 153 amino acids
Theoretical weight: 17.79 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62280 (Residues: 2-154; Coverage: 97%)
Gene name: RPS11
Sequence domains:
Small ribosomal subunit protein uS19 Chain: P
Molecule details ›
Chain: P
Length: 129 amino acids
Theoretical weight: 15.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 10-138; Coverage: 89%)
Gene names: RIG, RPS15
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS9 Chain: Q
Molecule details ›
Chain: Q
Length: 144 amino acids
Theoretical weight: 16.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 3-146; Coverage: 99%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17 Chain: R
Molecule details ›
Chain: R
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 uS13 Chain: S
Molecule details ›
Chain: S
Length: 145 amino acids
Theoretical weight: 17.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 1-145; Coverage: 95%)
Gene names: D6S218E, RPS18
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein eS19 Chain: T
Molecule details ›
Chain: T
Length: 143 amino acids
Theoretical weight: 15.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39019 (Residues: 2-144; Coverage: 99%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chain: U
Molecule details ›
Chain: U
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 eS21 Chain: V
Molecule details ›
Chain: V
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 uS12 Chain: X
Molecule details ›
Chain: X
Length: 141 amino acids
Theoretical weight: 15.63 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62266 (Residues: 2-142; Coverage: 99%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS26 Chain: a
Molecule details ›
Chain: a
Length: 102 amino acids
Theoretical weight: 11.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62854 (Residues: 2-103; Coverage: 89%)
Gene name: RPS26
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein eS28 Chain: c
Molecule details ›
Chain: c
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 uS14 Chain: d
Molecule details ›
Chain: d
Length: 55 amino acids
Theoretical weight: 6.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 2-56; Coverage: 98%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein RACK1 Chain: g
Molecule details ›
Chain: g
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 uS5 Chain: C
Molecule details ›
Chain: C
Length: 222 amino acids
Theoretical weight: 24.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P15880 (Residues: 59-280; Coverage: 76%)
Gene names: RPS2, RPS4
Sequence domains:
Small ribosomal subunit protein eS6 Chain: G
Molecule details ›
Chain: G
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 uS4 Chain: J
Molecule details ›
Chain: J
Length: 185 amino acids
Theoretical weight: 21.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46781 (Residues: 2-186; Coverage: 95%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein eS12 Chain: M
Molecule details ›
Chain: M
Length: 122 amino acids
Theoretical weight: 13.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 11-132; Coverage: 92%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS15 Chain: N
Molecule details ›
Chain: N
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 uS11 Chain: O
Molecule details ›
Chain: O
Length: 140 amino acids
Theoretical weight: 15.01 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62263 (Residues: 12-151; Coverage: 93%)
Gene names: PRO2640, RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS8 Chain: W
Molecule details ›
Chain: W
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 eS24 Chain: Y
Molecule details ›
Chain: Y
Length: 131 amino acids
Theoretical weight: 15.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62847 (Residues: 2-132; Coverage: 99%)
Gene name: RPS24
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS25 Chain: Z
Molecule details ›
Chain: Z
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 eS27 Chain: b
Molecule details ›
Chain: b
Length: 83 amino acids
Theoretical weight: 9.35 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42677 (Residues: 2-84; Coverage: 99%)
Gene names: MPS1, RPS27
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS30 Chain: e
Molecule details ›
Chain: e
Length: 42 amino acids
Theoretical weight: 4.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62861 (Residues: 76-117; Coverage: 32%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein eS31 Chain: f
Molecule details ›
Chain: f
Length: 67 amino acids
Theoretical weight: 7.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62979 (Residues: 85-151; Coverage: 43%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ribosomal protein S27a
Cell growth-regulating nucleolar protein Chain: y
Molecule details ›
Chain: y
Length: 72 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NX58 (Residues: 308-379; Coverage: 19%)
Gene names: LYAR, PNAS-5
Endothelial differentiation-related factor 1 Chain: i
Molecule details ›
Chain: i
Length: 110 amino acids
Theoretical weight: 12.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60869 (Residues: 24-133; Coverage: 74%)
Gene name: EDF1
Sequence domains:
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1740 nucleotides
Theoretical weight: 561.31 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
E-site tRNA Chain: x
Molecule details ›
Chain: x
Length: 75 nucleotides
Theoretical weight: 24 KDa
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand MG 30 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-11456

Quick links

Citations

17 review citations

Translational control of stem cell function.
Saba et al. (2021)
16 more

2 mentions without citation

EDF1 coordinates cellular responses to ribosome collisions.
Sinha et al. (2020)
1 more