› 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 3j7a coloured by chain and viewed from the front.
PDB 3j7a coloured by chain and viewed from the side.
PDB 3j7a coloured by chain and viewed from the top.
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 e03080 (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)
Entry contents:
31 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (33 distinct):
40S ribosomal protein S3a 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
40S ribosomal protein SA 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
KH type-2 domain-containing protein 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: Ribosomal protein S4/S9 N-terminal domain
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: Ribosomal family S4e
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
Ribosomal_S7 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
Ribosomal_S10 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
S10_plectin 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
40S ribosomal protein S12 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
Ribosomal_S13_N 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
Ribosomal_S17_N 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
40S ribosomal protein S30 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

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