› 7pwf

Electron Microscopy
2.85Å resolution

Cryo-EM structure of small subunit of Giardia lamblia ribosome at 2.9 A resolution

Released:
DOI: 10.2210/pdb7pwf/pdb
PDB entry 7pwf coloured by chain, front view.
PDB entry 7pwf coloured by chain, side view.
PDB entry 7pwf coloured by chain, top view.
Source organism: Giardia lamblia ATCC 50803
Primary publication:
Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia.
Hiregange DG, Rivalta A, Bose T, Breiner-Goldstein E, Samiya S, Cimicata G, Kulakova L, Zimmerman E, Bashan A, Herzberg O, Yonath A
Nucleic Acids Res 50 1770-1782 (2022)
PMID: 35100413
Related structures: EMD-13680

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
PDBe Complex ID:
PDB-CPX-105501 (preferred)
Entry contents:
31 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (32 distinct):
Ribosomal protein S29A Chain: d
Molecule details ›
Chain: d
Length: 137 amino acids
Theoretical weight: 15.5 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B7H6 (Residues: 1-137; Coverage: 100%)
Gene name: GL50803_39483
Sequence domains: Ribosomal protein S14p/S29e
Ribosomal protein S19e Chain: T
Molecule details ›
Chain: T
Length: 139 amino acids
Theoretical weight: 15.46 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A0A644F964 (Residues: 1-139; Coverage: 100%)
Gene name: GL50803_0060211
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 154 amino acids
Theoretical weight: 17.63 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BE02 (Residues: 1-154; Coverage: 100%)
Gene names: GL50803_0016652, GL50803_16652
Sequence domains:
Ribosomal protein S9 Chain: J
Molecule details ›
Chain: J
Length: 189 amino acids
Theoretical weight: 21.7 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BKS8 (Residues: 1-189; Coverage: 100%)
Gene names: GL50803_004547, GL50803_4547
Sequence domains:
40S ribosomal protein S3 Chain: D
Molecule details ›
Chain: D
Length: 217 amino acids
Theoretical weight: 24.78 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B8Z2 (Residues: 1-217; Coverage: 100%)
Gene names: GL50803_007999, GL50803_7999
Sequence domains: Ribosomal protein S3, C-terminal domain
Ribosomal protein S23 Chain: X
Molecule details ›
Chain: X
Length: 143 amino acids
Theoretical weight: 15.9 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BS96 (Residues: 1-143; Coverage: 100%)
Gene names: GL50803_0014699, GL50803_14699
Sequence domains: Ribosomal protein S12/S23
Ribosomal protein S18 Chain: S
Molecule details ›
Chain: S
Length: 154 amino acids
Theoretical weight: 17.51 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BZ58 (Residues: 1-154; Coverage: 100%)
Gene names: GL50803_0015551, GL50803_15551
Sequence domains: Ribosomal protein S13/S18
Ribosomal protein S16 Chain: Q
Molecule details ›
Chain: Q
Length: 158 amino acids
Theoretical weight: 17.63 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BKC6 (Residues: 1-158; Coverage: 100%)
Gene names: GL50803_004652, GL50803_4652
Sequence domains: Ribosomal protein S9/S16
S5 DRBM domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 242 amino acids
Theoretical weight: 26.77 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BMZ1 (Residues: 1-242; Coverage: 100%)
Gene names: GL50803_008118, GL50803_8118
Sequence domains:
Small ribosomal subunit protein uS2 Chain: A
Molecule details ›
Chain: A
Length: 245 amino acids
Theoretical weight: 28.1 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BE86 (Residues: 1-245; Coverage: 100%)
Gene name: GL50803_7766
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1 Chain: B
Molecule details ›
Chain: B
Length: 248 amino acids
Theoretical weight: 28.41 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BS79 (Residues: 1-248; Coverage: 100%)
Gene name: GL50803_16265
Sequence domains: Ribosomal S3Ae family
Ribosomal protein S24 Chain: Y
Molecule details ›
Chain: Y
Length: 132 amino acids
Theoretical weight: 14.87 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B593 (Residues: 1-132; Coverage: 100%)
Gene names: GL50803_0010367, GL50803_10367
Sequence domains: Ribosomal protein S24e
Ribosomal protein S27 Chain: b
Molecule details ›
Chain: b
Length: 124 amino acids
Theoretical weight: 14.12 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BJL1 (Residues: 1-124; Coverage: 100%)
Gene name: GL50803_10780
Sequence domains: Ribosomal protein S27
40S ribosomal protein S26 Chain: a
Molecule details ›
Chain: a
Length: 109 amino acids
Theoretical weight: 12.79 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BQZ7 (Residues: 1-109; Coverage: 100%)
Gene names: GL50803_0017364, GL50803_17364
Sequence domains: Ribosomal protein S26e
40S ribosomal protein S25 Chain: Z
Molecule details ›
Chain: Z
Length: 88 amino acids
Theoretical weight: 10.12 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B8H7 (Residues: 1-88; Coverage: 100%)
Gene names: GL50803_0013268, GL50803_13268
Sequence domains: S25 ribosomal protein
40S ribosomal protein S21 Chain: V
Molecule details ›
Chain: V
Length: 89 amino acids
Theoretical weight: 9.69 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B484 (Residues: 1-89; Coverage: 100%)
Gene names: GL50803_007082, GL50803_7082
Sequence domains: Ribosomal protein S21e
Ribosomal protein S15 Chain: P
Molecule details ›
Chain: P
Length: 145 amino acids
Theoretical weight: 16.73 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BBP3 (Residues: 1-145; Coverage: 100%)
Gene names: GL50803_0015260, GL50803_15260
Sequence domains: Ribosomal protein S19
Ribosomal protein S17 Chain: R
Molecule details ›
Chain: R
Length: 137 amino acids
Theoretical weight: 15.76 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BRG5 (Residues: 1-137; Coverage: 100%)
Gene names: GL50803_006135, GL50803_6135
Sequence domains: Ribosomal S17
Plectin/eS10 N-terminal domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 134 amino acids
Theoretical weight: 15.41 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BRX3 (Residues: 1-134; Coverage: 100%)
Gene names: GL50803_0010919, GL50803_10919
Sequence domains: Plectin/S10 domain
40S ribosomal protein S8 Chain: I
Molecule details ›
Chain: I
Length: 174 amino acids
Theoretical weight: 19.45 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B252 (Residues: 1-174; Coverage: 100%)
Gene names: GL50803_005845, GL50803_5845
Sequence domains: Ribosomal protein S8e
40S ribosomal protein S30 Chain: e
Molecule details ›
Chain: e
Length: 69 amino acids
Theoretical weight: 7.93 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A0A644F843 (Residues: 1-69; Coverage: 100%)
Gene name: GL50803_0060147
Sequence domains: Ribosomal protein S30
40S ribosomal protein S7 Chain: H
Molecule details ›
Chain: H
Length: 190 amino acids
Theoretical weight: 21.79 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BT38 (Residues: 1-190; Coverage: 100%)
Gene names: GL50803_0014329, GL50803_14329
Sequence domains: Ribosomal protein S7e
60S ribosomal protein L41 Chain: n
Molecule details ›
Chain: n
Length: 41 amino acids
Theoretical weight: 5.19 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: V6TX21 (Residues: 1-41; Coverage: 100%)
Gene name: GSB_151147
Sequence domains: Ribosomal protein L41
Ribosomal protein S28 Chain: c
Molecule details ›
Chain: c
Length: 64 amino acids
Theoretical weight: 7.36 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B4F3 (Residues: 1-64; Coverage: 100%)
Gene names: GL50803_003570, GL50803_3570
Sequence domains: Ribosomal protein S28e
Ribosomal protein S14 Chain: O
Molecule details ›
Chain: O
Length: 145 amino acids
Theoretical weight: 15.76 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: E2RU83 (Residues: 1-145; Coverage: 100%)
Gene names: GL50803_007878, GL50803_7878
Sequence domains: Ribosomal protein S11
Ribosomal protein S15A Chain: W
Molecule details ›
Chain: W
Length: 130 amino acids
Theoretical weight: 14.77 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: E2RU77 (Residues: 1-130; Coverage: 100%)
Gene names: GL50803_0015228, GL50803_15228
Sequence domains: Ribosomal protein S8
40S ribosomal protein S4 Chain: E
Molecule details ›
Chain: E
Length: 268 amino acids
Theoretical weight: 30.46 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BFE3 (Residues: 1-268; Coverage: 100%)
Gene names: GL50803_0011359, GL50803_11359
Sequence domains:
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 199 amino acids
Theoretical weight: 23.24 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: V6TVJ7 (Residues: 25-223; Coverage: 89%)
Gene name: GSB_14827
Sequence domains:
Small ribosomal subunit protein uS10 domain-containing protein Chain: U
Molecule details ›
Chain: U
Length: 126 amino acids
Theoretical weight: 14.07 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B4G0 (Residues: 1-126; Coverage: 100%)
Gene names: GL50803_006022, GL50803_6022
Sequence domains: Ribosomal protein S10p/S20e
40S ribosomal protein S6 Chain: G
Molecule details ›
Chain: G
Length: 248 amino acids
Theoretical weight: 28.08 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B6L8 (Residues: 1-248; Coverage: 100%)
Gene names: GL50803_0014620, GL50803_14620
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein uS7 domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 190 amino acids
Theoretical weight: 21.06 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BZD3 (Residues: 1-190; Coverage: 100%)
Gene names: GL50803_0012981, GL50803_12981
Sequence domains: Ribosomal protein S7p/S5e
rRNA 18S Chain: 2
Molecule details ›
Chain: 2
Length: 1452 nucleotides
Theoretical weight: 471.12 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand K 266 x K
Ligand MG 37 x MG
8 modified residues:
Ligand A2M 2 x A2M
Ligand OMC 1 x OMC
Ligand OMG 4 x OMG
Ligand 7MG 1 x 7MG
Ligand OMU 1 x OMU
Ligand 4OC 1 x 4OC
Ligand M7A 1 x M7A
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 2.85Å
Relevant EMDB volumes: EMD-13680

Quick links

Citations

2 review citations

The nucleolus of Giardia and its ribosomal biogenesis.
Lagunas-Rangel FA. (2023)
1 more

1 mention without citation

Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia.
Hiregange et al. (2022)