› 3j7a

Electron Microscopy
3.2Å resolution

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, small subunit

Released:
DOI: 10.2210/pdb3j7a/pdb
PDB entry 3j7a coloured by chain, front view.
PDB entry 3j7a coloured by chain, side view.
PDB entry 3j7a coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.
Wong W, Bai XC, Brown A, Fernandez IS, Hanssen E, Condron M, Tan YH, Baum J, Scheres SH
Elife 3 (2014)
PMID: 24913268
Related structures: EMD-2660

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 33-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-215639 (preferred)
Entry contents:
31 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (33 distinct):
Small ribosomal subunit protein eS1 Chain: B
Molecule details ›
Chain: B
Length: 262 amino acids
Theoretical weight: 30.11 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O97313 (Residues: 1-262; Coverage: 100%)
Gene names: MAL3P7.35, PF3D7_0322900, PFC1020c, RPS3A, eS1
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS2 Chain: C
Molecule details ›
Chain: C
Length: 263 amino acids
Theoretical weight: 29.89 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IJD4 (Residues: 1-263; Coverage: 100%)
Gene names: PF10_0264, PF3D7_1026800, RPS2, uS2
Sequence domains: Ribosomal protein S2
Structure domains: Glucose-6-phosphate isomerase like protein; domain 1
40S ribosomal protein S3 Chain: D
Molecule details ›
Chain: D
Length: 221 amino acids
Theoretical weight: 24.71 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IKH8 (Residues: 1-221; Coverage: 100%)
Gene name: PF3D7_1465900
Sequence domains:
Structure domains: Ribosomal protein S3, C-terminal domain
40S ribosomal protein S9, putative Chain: E
Molecule details ›
Chain: E
Length: 189 amino acids
Theoretical weight: 22.17 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8I3R0 (Residues: 1-189; Coverage: 100%)
Gene name: PF3D7_0520000
Sequence domains:
40S ribosomal protein S4 Chain: F
Molecule details ›
Chain: F
Length: 261 amino acids
Theoretical weight: 29.83 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IIU8 (Residues: 1-261; Coverage: 100%)
Gene name: PF3D7_1105400
Sequence domains:
Structure domains:
S5 DRBM domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 272 amino acids
Theoretical weight: 30.01 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IL02 (Residues: 1-272; Coverage: 100%)
Gene name: PF3D7_1447000
Sequence domains:
Structure domains:
40S ribosomal protein S6 Chain: H
Molecule details ›
Chain: H
Length: 306 amino acids
Theoretical weight: 35.47 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IDR9 (Residues: 1-306; Coverage: 100%)
Gene name: PF3D7_1342000
Sequence domains: Ribosomal protein S6e
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Small ribosomal subunit protein uS7 domain-containing protein Chain: I
Molecule details ›
Chain: I
Length: 195 amino acids
Theoretical weight: 21.9 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IBN5 (Residues: 1-195; Coverage: 100%)
Gene name: PF3D7_0721600
Sequence domains: Ribosomal protein S7p/S5e
Structure domains: Ribosomal protein S7 domain
40S ribosomal protein S7 Chain: J
Molecule details ›
Chain: J
Length: 194 amino acids
Theoretical weight: 22.52 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IET7 (Residues: 1-194; Coverage: 100%)
Gene name: PF3D7_1302800
Sequence domains: Ribosomal protein S7e
40S ribosomal protein S15A, putative Chain: K
Molecule details ›
Chain: K
Length: 130 amino acids
Theoretical weight: 14.9 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O77395 (Residues: 1-130; Coverage: 100%)
Gene name: PF3D7_0316800
Sequence domains: Ribosomal protein S8
Structure domains:
40S ribosomal protein S8 Chain: L
Molecule details ›
Chain: L
Length: 218 amino acids
Theoretical weight: 25.11 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IM10 (Residues: 1-218; Coverage: 100%)
Gene name: PF3D7_1408600
Sequence domains: Ribosomal protein S8e
40S ribosomal protein S16, putative Chain: M
Molecule details ›
Chain: M
Length: 144 amino acids
Theoretical weight: 16.32 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IAX5 (Residues: 1-144; Coverage: 100%)
Gene name: PF3D7_0813900
Sequence domains: Ribosomal protein S9/S16
Structure domains: Ribosomal Protein S5; domain 2
Small ribosomal subunit protein uS10 domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IK02 (Residues: 1-118; Coverage: 100%)
Gene name: PF3D7_1003500
Sequence domains: Ribosomal protein S10p/S20e
Structure domains: Ribosomal protein S10 domain
Plectin/eS10 N-terminal domain-containing protein Chain: O
Molecule details ›
Chain: O
Length: 137 amino acids
Theoretical weight: 16.51 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IBQ5 (Residues: 1-137; Coverage: 100%)
Gene name: PF3D7_0719700
Sequence domains: Plectin/S10 domain
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
40S ribosomal protein uS11 Chain: P
Molecule details ›
Chain: P
Length: 151 amino acids
Theoretical weight: 16.11 KDa
Source organism: Plasmodium falciparum 3D7
Structure domains: Ribosomal protein S11
40S ribosomal protein S23, putative Chain: Q
Molecule details ›
Chain: Q
Length: 145 amino acids
Theoretical weight: 16.17 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O97248 (Residues: 1-145; Coverage: 100%)
Gene name: PF3D7_0306900
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS12 Chain: R
Molecule details ›
Chain: R
Length: 141 amino acids
Theoretical weight: 15.41 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O97249 (Residues: 1-141; Coverage: 100%)
Gene names: MAL3P2.28, PF3D7_0307100, PFC0295C, RPS12, eS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
40S ribosomal protein S18, putative Chain: S
Molecule details ›
Chain: S
Length: 156 amino acids
Theoretical weight: 17.93 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IIA2 (Residues: 1-156; Coverage: 100%)
Gene name: PF3D7_1126200
Sequence domains: Ribosomal protein S13/S18
Structure domains: Helicase, Ruva Protein; domain 3
40S ribosomal protein S29, putative Chain: T
Molecule details ›
Chain: T
Length: 54 amino acids
Theoretical weight: 6.43 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C0H4K8 (Residues: 1-54; Coverage: 100%)
Gene name: PF3D7_0705700
Sequence domains: Ribosomal protein S14p/S29e
Structure domains: 30s Ribosomal Protein S14; Chain N
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: U
Molecule details ›
Chain: U
Length: 151 amino acids
Theoretical weight: 17.29 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IDB0 (Residues: 1-151; Coverage: 100%)
Gene name: PF3D7_1358800
Sequence domains:
Structure domains: S15/NS1, RNA-binding
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: V
Molecule details ›
Chain: V
Length: 161 amino acids
Theoretical weight: 18.8 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O77381 (Residues: 1-161; Coverage: 100%)
Gene name: PF3D7_0317600
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
40S ribosomal protein S17, putative Chain: W
Molecule details ›
Chain: W
Length: 137 amino acids
Theoretical weight: 16.1 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8I502 (Residues: 1-137; Coverage: 100%)
Gene name: PF3D7_1242700
Sequence domains: Ribosomal S17
Structure domains: Ribosomal protein S17e-like
40S ribosomal protein S19 Chain: X
Molecule details ›
Chain: X
Length: 145 amino acids
Theoretical weight: 16.8 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C0H5C2 (Residues: 1-145; Coverage: 100%)
Gene name: PF3D7_1317800
Sequence domains: Ribosomal protein S19
Structure domains: 30s Ribosomal Protein S19; Chain A
40S ribosomal protein S19 Chain: Y
Molecule details ›
Chain: Y
Length: 170 amino acids
Theoretical weight: 19.76 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IFP2 (Residues: 1-170; Coverage: 100%)
Gene name: PF3D7_0422400
Sequence domains: Ribosomal protein S19e
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
40S ribosomal protein S21 Chain: Z
Molecule details ›
Chain: Z
Length: 82 amino acids
Theoretical weight: 9.16 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IHS5 (Residues: 1-82; Coverage: 100%)
Gene name: PF3D7_1144000
Sequence domains: Ribosomal protein S21e
Structure domains: Hypothetical Cytosolic Protein; Chain: A;
40S ribosomal protein S24 Chain: 1
Molecule details ›
Chain: 1
Length: 133 amino acids
Theoretical weight: 15.43 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8I3R6 (Residues: 1-133; Coverage: 100%)
Gene name: PF3D7_0519400
Sequence domains: Ribosomal protein S24e
Structure domains: Alpha-Beta Plaits
40S ribosomal protein S25 Chain: 2
Molecule details ›
Chain: 2
Length: 105 amino acids
Theoretical weight: 11.69 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8ILN8 (Residues: 1-105; Coverage: 100%)
Gene name: PF3D7_1421200
Sequence domains: S25 ribosomal protein
40S ribosomal protein S26 Chain: 3
Molecule details ›
Chain: 3
Length: 107 amino acids
Theoretical weight: 12.54 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O96258 (Residues: 1-107; Coverage: 100%)
Gene name: PF3D7_0217800
Sequence domains: Ribosomal protein S26e
Structure domains: Ribosomal protein S26e
40S ribosomal protein S27 Chain: 4
Molecule details ›
Chain: 4
Length: 82 amino acids
Theoretical weight: 9.15 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IEN2 (Residues: 1-82; Coverage: 100%)
Gene name: PF3D7_1308300
Sequence domains: Ribosomal protein S27
Structure domains: Zn-binding ribosomal proteins
40S ribosomal protein S28e, putative Chain: 5
Molecule details ›
Chain: 5
Length: 67 amino acids
Theoretical weight: 7.51 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IKL9 (Residues: 1-67; Coverage: 100%)
Gene name: PF3D7_1461300
Sequence domains: Ribosomal protein S28e
Structure domains: Nucleic acid-binding proteins
Small ribosomal subunit protein eS30 Chain: 6
Molecule details ›
Chain: 6
Length: 58 amino acids
Theoretical weight: 6.51 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O96269 (Residues: 1-58; Coverage: 100%)
Gene names: PF3D7_0219200, PFB0885w, RPS30, eS30
Sequence domains: Ribosomal protein S30
18S Ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2092 nucleotides
Theoretical weight: 671.34 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
tRNA Chain: 7
Molecule details ›
Chain: 7
Length: 74 nucleotides
Theoretical weight: 23.77 KDa
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:
Ligand MG 67 x MG
Ligand 34G 1 x 34G
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-2660

Quick links

Citations

27 review citations

Advances in the field of single-particle cryo-electron microscopy over the last decade.
Frank J. (2017)
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13 mentions without citation

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Arenz et al. (2016)
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