› 3j79

Electron Microscopy
3.2Å resolution

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

Released:
DOI: 10.2210/pdb3j79/pdb
PDB entry 3j79 coloured by chain, front view.
PDB entry 3j79 coloured by chain, side view.
PDB entry 3j79 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 45-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110938 (preferred)
Entry contents:
42 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (45 distinct):
Large ribosomal subunit protein uL2 C-terminal domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 260 amino acids
Theoretical weight: 28.06 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8I3T9 (Residues: 1-260; Coverage: 100%)
Gene name: PF3D7_0516900
Sequence domains:
60S ribosomal protein L3 Chain: E
Molecule details ›
Chain: E
Length: 386 amino acids
Theoretical weight: 44.32 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IJC6 (Residues: 1-386; Coverage: 100%)
Gene name: PF3D7_1027800
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 C-terminal domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 411 amino acids
Theoretical weight: 46.31 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8I431 (Residues: 1-411; Coverage: 100%)
Gene name: PF3D7_0507100
Sequence domains:
60S ribosomal protein L11a, putative Chain: G
Molecule details ›
Chain: G
Length: 173 amino acids
Theoretical weight: 20.27 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IBQ6 (Residues: 1-173; Coverage: 100%)
Gene name: PF3D7_0719600
Sequence domains:
Large ribosomal subunit protein uL6 alpha-beta domain-containing protein Chain: H
Molecule details ›
Chain: H
Length: 190 amino acids
Theoretical weight: 21.64 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IE85 (Residues: 1-190; Coverage: 100%)
Gene name: PF3D7_1323100
Sequence domains: Ribosomal protein L6
60S ribosomal protein eL6 Chain: I
Molecule details ›
Chain: I
Length: 221 amino acids
Theoretical weight: 25.59 KDa
Source organism: Plasmodium falciparum 3D7
60S ribosomal protein L7a Chain: J
Molecule details ›
Chain: J
Length: 283 amino acids
Theoretical weight: 32.76 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8ILL2 (Residues: 1-283; Coverage: 100%)
Gene name: PF3D7_1424400
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L13, putative Chain: K
Molecule details ›
Chain: K
Length: 202 amino acids
Theoretical weight: 23.81 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IJZ7 (Residues: 1-202; Coverage: 100%)
Gene name: PF3D7_1004000
Sequence domains: Ribosomal protein L13
60S ribosomal protein L13 Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 25.51 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IAX6 (Residues: 1-215; Coverage: 100%)
Gene name: PF3D7_0814000
Sequence domains: Ribosomal protein L13e
60S ribosomal protein L23, putative Chain: M
Molecule details ›
Chain: M
Length: 139 amino acids
Theoretical weight: 15.02 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IE09 (Residues: 1-139; Coverage: 100%)
Gene name: PF3D7_1331800
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL14 domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 165 amino acids
Theoretical weight: 19.34 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8ILE8 (Residues: 1-165; Coverage: 100%)
Gene name: PF3D7_1431700
Sequence domains: Ribosomal protein L14
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: O
Molecule details ›
Chain: O
Length: 148 amino acids
Theoretical weight: 16.77 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C6KT23 (Residues: 1-148; Coverage: 100%)
Gene name: PF3D7_0618300
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Ribosomal protein L15 Chain: P
Molecule details ›
Chain: P
Length: 205 amino acids
Theoretical weight: 24.2 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C0H4A6 (Residues: 1-205; Coverage: 100%)
Gene name: PF3D7_0415900
Sequence domains: Ribosomal L15
60S ribosomal protein L10, putative Chain: Q
Molecule details ›
Chain: Q
Length: 219 amino acids
Theoretical weight: 25.27 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8ILV2 (Residues: 1-219; Coverage: 100%)
Gene name: PF3D7_1414300
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein Chain: R
Molecule details ›
Chain: R
Length: 294 amino acids
Theoretical weight: 34.07 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8ILL3 (Residues: 1-294; Coverage: 100%)
Gene name: PF3D7_1424100
Sequence domains:
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: S
Molecule details ›
Chain: S
Length: 187 amino acids
Theoretical weight: 21.51 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C0H5G3 (Residues: 1-187; Coverage: 100%)
Gene name: PF3D7_1341300
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19 domain-containing protein Chain: T
Molecule details ›
Chain: T
Length: 182 amino acids
Theoretical weight: 21.64 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C6KSY6 (Residues: 1-182; Coverage: 100%)
Gene name: PF3D7_0614500
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L18a Chain: U
Molecule details ›
Chain: U
Length: 184 amino acids
Theoretical weight: 21.79 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IDS6 (Residues: 1-184; Coverage: 100%)
Gene name: PF3D7_1341200
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
60S ribosomal protein L21 Chain: V
Molecule details ›
Chain: V
Length: 161 amino acids
Theoretical weight: 18.84 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8ILK3 (Residues: 1-161; Coverage: 100%)
Gene name: PF3D7_1426000
Sequence domains: Ribosomal protein L21e
60S ribosomal protein L17, putative Chain: W
Molecule details ›
Chain: W
Length: 203 amino acids
Theoretical weight: 23.47 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IDI5 (Residues: 1-203; Coverage: 100%)
Gene name: PF3D7_1351400
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL22 Chain: X
Molecule details ›
Chain: X
Length: 139 amino acids
Theoretical weight: 16.42 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IB51 (Residues: 1-139; Coverage: 100%)
Gene name: PF3D7_0821700
Sequence domains: Ribosomal L22e protein family
Large ribosomal subunit protein uL23 N-terminal domain-containing protein Chain: Y
Molecule details ›
Chain: Y
Length: 190 amino acids
Theoretical weight: 22.15 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IE82 (Residues: 1-190; Coverage: 100%)
Gene name: PF3D7_1323400
Sequence domains:
KOW domain-containing protein Chain: Z
Molecule details ›
Chain: Z
Length: 126 amino acids
Theoretical weight: 14.86 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O77364 (Residues: 1-126; Coverage: 100%)
Gene name: PF3D7_0312800
Sequence domains:
60S ribosomal protein L24, putative Chain: 0
Molecule details ›
Chain: 0
Length: 162 amino acids
Theoretical weight: 19.3 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IEM3 (Residues: 1-162; Coverage: 100%)
Gene name: PF3D7_1309100
Sequence domains: Ribosomal protein L24e
60S ribosomal protein L27 Chain: 1
Molecule details ›
Chain: 1
Length: 146 amino acids
Theoretical weight: 16.79 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IKM5 (Residues: 1-146; Coverage: 100%)
Gene name: PF3D7_1460700
Sequence domains: Ribosomal L27e protein family
Ribosomal eL28/Mak16 domain-containing protein Chain: 2
Molecule details ›
Chain: 2
Length: 127 amino acids
Theoretical weight: 14.44 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IHU0 (Residues: 1-127; Coverage: 100%)
Gene name: PF3D7_1142500
Sequence domains: Ribosomal L28e protein family
60S ribosomal protein L35, putative Chain: 3
Molecule details ›
Chain: 3
Length: 124 amino acids
Theoretical weight: 14.79 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IIB4 (Residues: 1-124; Coverage: 100%)
Gene name: PF3D7_1124900
Sequence domains: Ribosomal L29 protein
60S ribosomal protein L29 Chain: 4
Molecule details ›
Chain: 4
Length: 67 amino acids
Theoretical weight: 8.04 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C6S3J6 (Residues: 1-67; Coverage: 100%)
Gene name: PF3D7_1460300
Sequence domains: Ribosomal L29e protein family
60S ribosomal protein L7, putative Chain: 5
Molecule details ›
Chain: 5
Length: 257 amino acids
Theoretical weight: 30.59 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O97250 (Residues: 1-257; Coverage: 100%)
Gene name: PF3D7_0307200
Sequence domains:
Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein Chain: 6
Molecule details ›
Chain: 6
Length: 108 amino acids
Theoretical weight: 11.79 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IJK8 (Residues: 1-108; Coverage: 100%)
Gene name: PF3D7_1019400
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L31 Chain: 7
Molecule details ›
Chain: 7
Length: 120 amino acids
Theoretical weight: 14.1 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8I463 (Residues: 1-120; Coverage: 100%)
Gene name: PF3D7_0503800
Sequence domains: Ribosomal protein L31e
60S ribosomal protein L32 Chain: 8
Molecule details ›
Chain: 8
Length: 131 amino acids
Theoretical weight: 15.57 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8I3B0 (Residues: 1-131; Coverage: 100%)
Gene name: PF3D7_0903900
Sequence domains: Ribosomal protein L32
60S ribosomal protein L35ae, putative Chain: 9
Molecule details ›
Chain: 9
Length: 140 amino acids
Theoretical weight: 16.31 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IHT9 (Residues: 1-140; Coverage: 100%)
Gene name: PF3D7_1142600
Sequence domains: Ribosomal protein L35Ae
60S ribosomal protein L34 Chain: a
Molecule details ›
Chain: a
Length: 150 amino acids
Theoretical weight: 17.41 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8IBY4 (Residues: 1-150; Coverage: 100%)
Gene name: PF3D7_0710600
Sequence domains: Ribosomal protein L34e
60S ribosomal protein L36 Chain: b
Molecule details ›
Chain: b
Length: 112 amino acids
Theoretical weight: 12.83 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8I713 (Residues: 1-112; Coverage: 100%)
Gene name: PF3D7_1109900
Sequence domains: Ribosomal protein L36e
Ribosomal protein L37 Chain: c
Molecule details ›
Chain: c
Length: 92 amino acids
Theoretical weight: 10.57 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C0H4L5 (Residues: 1-92; Coverage: 100%)
Gene name: PF3D7_0706400
Sequence domains: Ribosomal protein L37e
60S ribosomal protein L38 Chain: d
Molecule details ›
Chain: d
Length: 87 amino acids
Theoretical weight: 10.34 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8II62 (Residues: 1-87; Coverage: 100%)
Gene name: PF3D7_1130100
Sequence domains: Ribosomal L38e protein family
60S ribosomal protein L39 Chain: e
Molecule details ›
Chain: e
Length: 51 amino acids
Theoretical weight: 6.54 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C0H4H3 (Residues: 1-51; Coverage: 100%)
Gene name: PF3D7_0611700
Sequence domains: Ribosomal L39 protein
Ubiquitin-like domain-containing protein Chain: f
Molecule details ›
Chain: f
Length: 128 amino acids
Theoretical weight: 14.65 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: Q8ID50 (Residues: 1-128; Coverage: 100%)
Gene name: PF3D7_1365900
Sequence domains:
60S ribosomal protein L41 Chain: g
Molecule details ›
Chain: g
Length: 39 amino acids
Theoretical weight: 5.11 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: C6S3G4 (Residues: 1-39; Coverage: 100%)
Gene name: PF3D7_1144300
Sequence domains: Ribosomal protein L41
Large ribosomal subunit protein eL43 Chain: h
Molecule details ›
Chain: h
Length: 96 amino acids
Theoretical weight: 10.83 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O96184 (Residues: 1-96; Coverage: 100%)
Gene names: PF3D7_0210100, PFB0455w, RPL37A, eL43
Sequence domains: Ribosomal L37ae protein family
Large ribosomal subunit protein eL42 Chain: i
Molecule details ›
Chain: i
Length: 104 amino acids
Theoretical weight: 12.19 KDa
Source organism: Plasmodium falciparum 3D7
UniProt:
  • Canonical: O97231 (Residues: 1-104; Coverage: 100%)
Gene names: MAL3P2.9, PF3D7_0304400, PFC0200W, RPL44, eL44
Sequence domains: Ribosomal protein L44
28S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 3788 nucleotides
Theoretical weight: 1216.21 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 119 nucleotides
Theoretical weight: 38.41 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: C
Molecule details ›
Chain: C
Length: 159 nucleotides
Theoretical weight: 51.21 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 163 x MG
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

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

Quick links

Citations

29 review citations

Advances in the field of single-particle cryo-electron microscopy over the last decade.
Frank J. (2017)
28 more

14 mentions without citation

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.
Kimanius et al. (2016)
13 more