› 7pwo

Electron Microscopy
2.75Å resolution

Cryo-EM structure of Giardia lamblia ribosome at 2.75 A resolution

Released:
DOI: 10.2210/pdb7pwo/pdb
PDB entry 7pwo coloured by chain, front view.
PDB entry 7pwo coloured by chain, side view.
PDB entry 7pwo 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
OpenAccess logo Nucleic Acids Res 50 1770-1782 (2022)
PMID: 35100413
Related structures: EMD-13683

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 74-mer (preferred)
PDBe Complex ID:
PDB-CPX-252168 (preferred)
Entry contents:
68 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (74 distinct):
Ribosomal protein S19e Chain: T1
Molecule details ›
Chain: T1
Length: 139 amino acids
Theoretical weight: 15.46 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S13 Chain: N1
Molecule details ›
Chain: N1
Length: 154 amino acids
Theoretical weight: 17.63 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S9 Chain: J1
Molecule details ›
Chain: J1
Length: 189 amino acids
Theoretical weight: 21.7 KDa
Source organism: Giardia lamblia ATCC 50803
40S ribosomal protein S3 Chain: D1
Molecule details ›
Chain: D1
Length: 217 amino acids
Theoretical weight: 24.78 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S23 Chain: X1
Molecule details ›
Chain: X1
Length: 143 amino acids
Theoretical weight: 15.9 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S18 Chain: S1
Molecule details ›
Chain: S1
Length: 154 amino acids
Theoretical weight: 17.51 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S16 Chain: Q1
Molecule details ›
Chain: Q1
Length: 158 amino acids
Theoretical weight: 17.63 KDa
Source organism: Giardia lamblia ATCC 50803
Small ribosomal subunit protein uS5 Chain: C1
Molecule details ›
Chain: C1
Length: 242 amino acids
Theoretical weight: 26.77 KDa
Source organism: Giardia lamblia ATCC 50803
Small ribosomal subunit protein eS1 Chain: B1
Molecule details ›
Chain: B1
Length: 248 amino acids
Theoretical weight: 28.41 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S27 Chain: b1
Molecule details ›
Chain: b1
Length: 124 amino acids
Theoretical weight: 14.12 KDa
Source organism: Giardia lamblia ATCC 50803
40S ribosomal protein S26 Chain: a1
Molecule details ›
Chain: a1
Length: 109 amino acids
Theoretical weight: 12.79 KDa
Source organism: Giardia lamblia ATCC 50803
40S ribosomal protein S21 Chain: V1
Molecule details ›
Chain: V1
Length: 89 amino acids
Theoretical weight: 9.69 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S17 Chain: R1
Molecule details ›
Chain: R1
Length: 137 amino acids
Theoretical weight: 15.76 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S10B Chain: K1
Molecule details ›
Chain: K1
Length: 134 amino acids
Theoretical weight: 15.41 KDa
Source organism: Giardia lamblia ATCC 50803
40S ribosomal protein S8 Chain: I1
Molecule details ›
Chain: I1
Length: 174 amino acids
Theoretical weight: 19.45 KDa
Source organism: Giardia lamblia ATCC 50803
40S ribosomal protein S30 Chain: e1
Molecule details ›
Chain: e1
Length: 69 amino acids
Theoretical weight: 7.93 KDa
Source organism: Giardia lamblia ATCC 50803
40S ribosomal protein S7 Chain: H1
Molecule details ›
Chain: H1
Length: 190 amino acids
Theoretical weight: 21.79 KDa
Source organism: Giardia lamblia ATCC 50803
60S ribosomal protein L41 Chain: n1
Molecule details ›
Chain: n1
Length: 41 amino acids
Theoretical weight: 5.19 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S28 Chain: c1
Molecule details ›
Chain: c1
Length: 64 amino acids
Theoretical weight: 7.36 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S14 Chain: O1
Molecule details ›
Chain: O1
Length: 145 amino acids
Theoretical weight: 15.76 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S15A Chain: W1
Molecule details ›
Chain: W1
Length: 130 amino acids
Theoretical weight: 14.77 KDa
Source organism: Giardia lamblia ATCC 50803
40S ribosomal protein S4 Chain: E1
Molecule details ›
Chain: E1
Length: 268 amino acids
Theoretical weight: 30.46 KDa
Source organism: Giardia lamblia ATCC 50803
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: L1
Molecule details ›
Chain: L1
Length: 199 amino acids
Theoretical weight: 23.24 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S20 Chain: U1
Molecule details ›
Chain: U1
Length: 126 amino acids
Theoretical weight: 14.07 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L8 Chain: A2
Molecule details ›
Chain: A2
Length: 251 amino acids
Theoretical weight: 27.09 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L3 Chain: B2
Molecule details ›
Chain: B2
Length: 379 amino acids
Theoretical weight: 42.72 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L4 Chain: C2
Molecule details ›
Chain: C2
Length: 316 amino acids
Theoretical weight: 35.05 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L5 Chain: D2
Molecule details ›
Chain: D2
Length: 297 amino acids
Theoretical weight: 33.96 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L7 Chain: F2
Molecule details ›
Chain: F2
Length: 235 amino acids
Theoretical weight: 27.1 KDa
Source organism: Giardia lamblia ATCC 50803
60S ribosomal protein L7a Chain: G2
Molecule details ›
Chain: G2
Length: 225 amino acids
Theoretical weight: 25.43 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L6 Chain: H2
Molecule details ›
Chain: H2
Length: 185 amino acids
Theoretical weight: 20.89 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L10 Chain: I2
Molecule details ›
Chain: I2
Length: 210 amino acids
Theoretical weight: 24.28 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L11 Chain: J2
Molecule details ›
Chain: J2
Length: 173 amino acids
Theoretical weight: 19.77 KDa
Source organism: Giardia lamblia ATCC 50803
60S ribosomal protein L13 Chain: L2
Molecule details ›
Chain: L2
Length: 234 amino acids
Theoretical weight: 26.64 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L14 Chain: M2
Molecule details ›
Chain: M2
Length: 131 amino acids
Theoretical weight: 14.79 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L15 Chain: N2
Molecule details ›
Chain: N2
Length: 204 amino acids
Theoretical weight: 24.35 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L13a Chain: O2
Molecule details ›
Chain: O2
Length: 197 amino acids
Theoretical weight: 22.92 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L17 Chain: P2
Molecule details ›
Chain: P2
Length: 164 amino acids
Theoretical weight: 18.72 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L18 Chain: Q2
Molecule details ›
Chain: Q2
Length: 179 amino acids
Theoretical weight: 20.21 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L19 Chain: R2
Molecule details ›
Chain: R2
Length: 196 amino acids
Theoretical weight: 23.2 KDa
Source organism: Giardia lamblia ATCC 50803
60S ribosomal protein L18a Chain: S2
Molecule details ›
Chain: S2
Length: 173 amino acids
Theoretical weight: 20.62 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L21 Chain: T2
Molecule details ›
Chain: T2
Length: 159 amino acids
Theoretical weight: 18.3 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein eL22 Chain: U2
Molecule details ›
Chain: U2
Length: 171 amino acids
Theoretical weight: 19.94 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L23 Chain: V2
Molecule details ›
Chain: V2
Length: 142 amino acids
Theoretical weight: 15.45 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L23A Chain: X2
Molecule details ›
Chain: X2
Length: 141 amino acids
Theoretical weight: 16.05 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L26 Chain: Y2
Molecule details ›
Chain: Y2
Length: 135 amino acids
Theoretical weight: 15.62 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L27 Chain: Z2
Molecule details ›
Chain: Z2
Length: 135 amino acids
Theoretical weight: 15.37 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L27a Chain: a2
Molecule details ›
Chain: a2
Length: 149 amino acids
Theoretical weight: 17.17 KDa
Source organism: Giardia lamblia ATCC 50803
60S ribosomal protein L29 Chain: b2
Molecule details ›
Chain: b2
Length: 62 amino acids
Theoretical weight: 7.36 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L30 Chain: c2
Molecule details ›
Chain: c2
Length: 109 amino acids
Theoretical weight: 11.7 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L31e Chain: d2
Molecule details ›
Chain: d2
Length: 106 amino acids
Theoretical weight: 12.18 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L32 Chain: e2
Molecule details ›
Chain: e2
Length: 136 amino acids
Theoretical weight: 15.99 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L35a Chain: f2
Molecule details ›
Chain: f2
Length: 123 amino acids
Theoretical weight: 13.91 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L34 Chain: g2
Molecule details ›
Chain: g2
Length: 120 amino acids
Theoretical weight: 13.53 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L35 Chain: h2
Molecule details ›
Chain: h2
Length: 124 amino acids
Theoretical weight: 14.29 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L36e Chain: i2
Molecule details ›
Chain: i2
Length: 90 amino acids
Theoretical weight: 10.59 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L37 Chain: j2
Molecule details ›
Chain: j2
Length: 89 amino acids
Theoretical weight: 10.33 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal L38e Chain: k2
Molecule details ›
Chain: k2
Length: 77 amino acids
Theoretical weight: 8.61 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L39 Chain: l2
Molecule details ›
Chain: l2
Length: 51 amino acids
Theoretical weight: 6.35 KDa
Source organism: Giardia lamblia ATCC 50803
50S ribosomal protein L40e Chain: m2
Molecule details ›
Chain: m2
Length: 127 amino acids
Theoretical weight: 14.34 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L44 Chain: o2
Molecule details ›
Chain: o2
Length: 106 amino acids
Theoretical weight: 12.31 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L37a Chain: p2
Molecule details ›
Chain: p2
Length: 94 amino acids
Theoretical weight: 10.51 KDa
Source organism: Giardia lamblia ATCC 50803
Large ribosomal subunit protein eL24-related N-terminal domain-containing protein Chain: W2
Molecule details ›
Chain: W2
Length: 102 amino acids
Theoretical weight: 12.01 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S29A Chain: d1
Molecule details ›
Chain: d1
Length: 137 amino acids
Theoretical weight: 15.5 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S5 Chain: F1
Molecule details ›
Chain: F1
Length: 190 amino acids
Theoretical weight: 21.06 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein S24 Chain: Y1
Molecule details ›
Chain: Y1
Length: 132 amino acids
Theoretical weight: 14.87 KDa
Source organism: Giardia lamblia ATCC 50803
40S ribosomal protein S6 Chain: G1
Molecule details ›
Chain: G1
Length: 248 amino acids
Theoretical weight: 28.08 KDa
Source organism: Giardia lamblia ATCC 50803
Small ribosomal subunit protein uS2 Chain: A1
Molecule details ›
Chain: A1
Length: 245 amino acids
Theoretical weight: 28.1 KDa
Source organism: Giardia lamblia ATCC 50803
rRNA 28S Chain: 1
Molecule details ›
Chain: 1
Length: 2707 nucleotides
Theoretical weight: 878.24 KDa
Source organism: Giardia lamblia ATCC 50803
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: 3
Molecule details ›
Chain: 3
Length: 120 nucleotides
Theoretical weight: 38.67 KDa
Source organism: Giardia lamblia ATCC 50803
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: 42
Molecule details ›
Chain: 42
Length: 139 nucleotides
Theoretical weight: 44.97 KDa
Source organism: Giardia lamblia ATCC 50803
E-site tRNA Chain: w2
Molecule details ›
Chain: w2
Length: 14 nucleotides
Theoretical weight: 4.46 KDa
Source organism: Giardia lamblia ATCC 50803
P-site tRNA Chain: E
Molecule details ›
Chain: E
Length: 3 nucleotides
Theoretical weight: 895 Da
Source organism: Giardia lamblia ATCC 50803
rRNA 18S Chain: 2
Molecule details ›
Chain: 2
Length: 1452 nucleotides
Theoretical weight: 471.12 KDa
Source organism: Giardia lamblia ATCC 50803
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand K 455 x K
Ligand MG 101 x MG
9 modified residues:
Ligand OMU 5 x OMU
Ligand OMG 16 x OMG
Ligand A2M 6 x A2M
Ligand OMC 4 x OMC
Ligand 5MC 2 x 5MC
Ligand 7MG 1 x 7MG
Ligand 4OC 1 x 4OC
Ligand M7A 1 x M7A
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 2.75Å
Relevant EMDB volumes: EMD-13683

Quick links

Citations

3 review citations

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

1 mention without citation

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