› 7pwg

Electron Microscopy
2.75Å resolution

Cryo-EM structure of large subunit of Giardia lamblia ribosome at 2.7 A resolution

Released:
DOI: 10.2210/pdb7pwg/pdb
PDB entry 7pwg coloured by chain, front view.
PDB entry 7pwg coloured by chain, side view.
PDB entry 7pwg 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-13681

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 44-mer (preferred)
PDBe Complex ID:
PDB-CPX-279043 (preferred)
Entry contents:
39 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (44 distinct):
Ribosomal protein L8 Chain: A
Molecule details ›
Chain: A
Length: 251 amino acids
Theoretical weight: 27.09 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: E2RTN4 (Residues: 1-251; Coverage: 100%)
Gene name: GL50803_0016086
Sequence domains:
Ribosomal protein L3 Chain: B
Molecule details ›
Chain: B
Length: 379 amino acids
Theoretical weight: 42.72 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BRZ3 (Residues: 1-379; Coverage: 100%)
Gene name: GL50803_0016525
Sequence domains: Ribosomal protein L3
Ribosomal protein L4 Chain: C
Molecule details ›
Chain: C
Length: 316 amino acids
Theoretical weight: 35.05 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B7H8 (Residues: 1-316; Coverage: 100%)
Gene name: GL50803_0017547
Sequence domains:
Ribosomal protein L5 Chain: D
Molecule details ›
Chain: D
Length: 297 amino acids
Theoretical weight: 33.96 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: E2RU47 (Residues: 1-297; Coverage: 100%)
Gene name: GL50803_0017395
Sequence domains:
Ribosomal protein L7 Chain: F
Molecule details ›
Chain: F
Length: 235 amino acids
Theoretical weight: 27.1 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BRY6 (Residues: 1-235; Coverage: 100%)
Gene name: GL50803_0019436
Sequence domains: Ribosomal protein L30p/L7e
60S ribosomal protein L7a Chain: G
Molecule details ›
Chain: G
Length: 225 amino acids
Theoretical weight: 25.43 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BLL7 (Residues: 1-225; Coverage: 100%)
Gene name: GL50803_0017244
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ribosomal protein L6 Chain: H
Molecule details ›
Chain: H
Length: 185 amino acids
Theoretical weight: 20.89 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BNT5 (Residues: 1-185; Coverage: 100%)
Gene name: GL50803_0017056
Sequence domains: Ribosomal protein L6
Ribosomal protein L10 Chain: I
Molecule details ›
Chain: I
Length: 210 amino acids
Theoretical weight: 24.28 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BM86 (Residues: 1-210; Coverage: 100%)
Gene name: GL50803_0010428
Sequence domains: Ribosomal protein L16p/L10e
Ribosomal protein L11 Chain: J
Molecule details ›
Chain: J
Length: 173 amino acids
Theoretical weight: 19.77 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BI95 (Residues: 1-173; Coverage: 100%)
Gene name: GL50803_005593
Sequence domains:
60S ribosomal protein L13 Chain: L
Molecule details ›
Chain: L
Length: 234 amino acids
Theoretical weight: 26.64 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L14 Chain: M
Molecule details ›
Chain: M
Length: 131 amino acids
Theoretical weight: 14.79 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B4F8 (Residues: 1-131; Coverage: 100%)
Gene name: GL50803_0014091
Sequence domains: Ribosomal protein L14
Ribosomal protein L15 Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 24.35 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B8Z6 (Residues: 1-204; Coverage: 100%)
Gene name: GL50803_008001
Sequence domains: Ribosomal L15
Ribosomal protein L13a Chain: O
Molecule details ›
Chain: O
Length: 197 amino acids
Theoretical weight: 22.92 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BU75 (Residues: 1-197; Coverage: 100%)
Gene name: GL50803_0011247
Sequence domains: Ribosomal protein L13
Ribosomal protein L17 Chain: P
Molecule details ›
Chain: P
Length: 164 amino acids
Theoretical weight: 18.72 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BE76 (Residues: 1-164; Coverage: 100%)
Gene name: GL50803_0098056
Sequence domains: Ribosomal protein L22p/L17e
Ribosomal protein L18 Chain: Q
Molecule details ›
Chain: Q
Length: 179 amino acids
Theoretical weight: 20.21 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B4T7 (Residues: 1-179; Coverage: 100%)
Gene name: GL50803_0011950
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Ribosomal protein L19 Chain: R
Molecule details ›
Chain: R
Length: 196 amino acids
Theoretical weight: 23.2 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BH61 (Residues: 1-196; Coverage: 100%)
Gene name: GL50803_0016431
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L18a Chain: S
Molecule details ›
Chain: S
Length: 173 amino acids
Theoretical weight: 20.62 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L21 Chain: T
Molecule details ›
Chain: T
Length: 159 amino acids
Theoretical weight: 18.3 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B2Q4 (Residues: 1-159; Coverage: 100%)
Gene name: GL50803_0015520
Sequence domains: Ribosomal protein L21e
Ribosomal protein eL22 Chain: U
Molecule details ›
Chain: U
Length: 171 amino acids
Theoretical weight: 19.94 KDa
Source organism: Giardia lamblia ATCC 50803
Ribosomal protein L23 Chain: V
Molecule details ›
Chain: V
Length: 142 amino acids
Theoretical weight: 15.45 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BS37 (Residues: 1-142; Coverage: 100%)
Gene name: GL50803_0010091
Sequence domains: Ribosomal protein L14p/L23e
Ribosomal protein L23A Chain: X
Molecule details ›
Chain: X
Length: 141 amino acids
Theoretical weight: 16.05 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BMP6 (Residues: 1-141; Coverage: 100%)
Gene name: GL50803_007870
Sequence domains:
Ribosomal protein L26 Chain: Y
Molecule details ›
Chain: Y
Length: 135 amino acids
Theoretical weight: 15.62 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BFT3 (Residues: 1-135; Coverage: 100%)
Gene name: GL50803_0015046
Sequence domains: Ribosomal proteins L26 eukaryotic, L24P archaeal
Ribosomal protein L27 Chain: Z
Molecule details ›
Chain: Z
Length: 135 amino acids
Theoretical weight: 15.37 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B1T3 (Residues: 1-135; Coverage: 100%)
Gene name: GL50803_008462
Sequence domains:
Ribosomal protein L27a Chain: a
Molecule details ›
Chain: a
Length: 149 amino acids
Theoretical weight: 17.17 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BZ78 (Residues: 1-149; Coverage: 100%)
Gene name: GL50803_0016310
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
60S ribosomal protein L29 Chain: b
Molecule details ›
Chain: b
Length: 62 amino acids
Theoretical weight: 7.36 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BYY2 (Residues: 1-62; Coverage: 100%)
Gene name: GL50803_0014457
Sequence domains: Ribosomal L29e protein family
Ribosomal protein L30 Chain: c
Molecule details ›
Chain: c
Length: 109 amino acids
Theoretical weight: 11.7 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B5N7 (Residues: 1-109; Coverage: 100%)
Gene name: GL50803_0014321
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ribosomal protein L31e Chain: d
Molecule details ›
Chain: d
Length: 106 amino acids
Theoretical weight: 12.18 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BMP3 (Residues: 1-106; Coverage: 100%)
Gene name: GL50803_0016368
Sequence domains: Ribosomal protein L31e
Ribosomal protein L32 Chain: e
Molecule details ›
Chain: e
Length: 136 amino acids
Theoretical weight: 15.99 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BMD9 (Residues: 1-136; Coverage: 100%)
Gene name: GL50803_0014049
Sequence domains: Ribosomal protein L32
Ribosomal protein L35a Chain: f
Molecule details ›
Chain: f
Length: 123 amino acids
Theoretical weight: 13.91 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BKK5 (Residues: 1-123; Coverage: 100%)
Gene name: GL50803_005947
Sequence domains: Ribosomal protein L35Ae
Ribosomal protein L34 Chain: g
Molecule details ›
Chain: g
Length: 120 amino acids
Theoretical weight: 13.53 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BMF7 (Residues: 1-120; Coverage: 100%)
Gene name: GL50803_0036069
Sequence domains: Ribosomal protein L34e
Ribosomal protein L29 Chain: h
Molecule details ›
Chain: h
Length: 124 amino acids
Theoretical weight: 14.29 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A0A644FBK5 (Residues: 1-124; Coverage: 100%)
Gene name: GL50803_006133
Sequence domains: Ribosomal L29 protein
Ribosomal protein L36e Chain: i
Molecule details ›
Chain: i
Length: 90 amino acids
Theoretical weight: 10.59 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BYA6 (Residues: 1-90; Coverage: 100%)
Gene name: GL50803_0016114
Sequence domains: Ribosomal protein L36e
Ribosomal protein L37 Chain: j
Molecule details ›
Chain: j
Length: 89 amino acids
Theoretical weight: 10.33 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BLV7 (Residues: 1-89; Coverage: 100%)
Gene name: GL50803_0014171
Sequence domains: Ribosomal protein L37e
Ribosomal L38e Chain: k
Molecule details ›
Chain: k
Length: 77 amino acids
Theoretical weight: 8.61 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8B481 (Residues: 1-77; Coverage: 100%)
Gene name: GL50803_0034093
Sequence domains: Ribosomal L38e protein family
Ribosomal protein L39 Chain: l
Molecule details ›
Chain: l
Length: 51 amino acids
Theoretical weight: 6.35 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A0A644EZB9 (Residues: 1-51; Coverage: 100%)
Gene name: GL50803_0060191
Sequence domains: Ribosomal L39 protein
50S ribosomal protein L40e Chain: m
Molecule details ›
Chain: m
Length: 127 amino acids
Theoretical weight: 14.34 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BXE1 (Residues: 1-127; Coverage: 100%)
Gene name: GL50803_005665
Sequence domains:
Ribosomal protein L44 Chain: o
Molecule details ›
Chain: o
Length: 106 amino acids
Theoretical weight: 12.31 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BQU8 (Residues: 1-106; Coverage: 100%)
Gene name: GL50803_009810
Sequence domains: Ribosomal protein L44
Ribosomal protein L37a Chain: p
Molecule details ›
Chain: p
Length: 94 amino acids
Theoretical weight: 10.51 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BN26 (Residues: 1-94; Coverage: 100%)
Gene name: GL50803_005517
Sequence domains: Ribosomal L37ae protein family
Large ribosomal subunit protein eL24-related N-terminal domain-containing protein Chain: W
Molecule details ›
Chain: W
Length: 102 amino acids
Theoretical weight: 12.01 KDa
Source organism: Giardia lamblia ATCC 50803
UniProt:
  • Canonical: A8BRH7 (Residues: 1-102; Coverage: 100%)
Gene name: GL50803_0019003
Sequence domains: Ribosomal protein L24e
rRNA 28S Chain: 1
Molecule details ›
Chain: 1
Length: 2707 nucleotides
Theoretical weight: 878.25 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: 3
Molecule details ›
Chain: 3
Length: 120 nucleotides
Theoretical weight: 38.67 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: 4
Molecule details ›
Chain: 4
Length: 139 nucleotides
Theoretical weight: 44.97 KDa
E-site tRNA Chain: w
Molecule details ›
Chain: w
Length: 76 nucleotides
Theoretical weight: 24.5 KDa
Sequence domains: tRNA
P-site tRNA Chain: E
Molecule details ›
Chain: E
Length: 3 nucleotides
Theoretical weight: 895 Da

Ligands and Environments

3 bound ligands:
Ligand MG 112 x MG
Ligand K 181 x K
Ligand PGE 1 x PGE
5 modified residues:
Ligand OMU 4 x OMU
Ligand OMG 12 x OMG
Ligand A2M 4 x A2M
Ligand OMC 3 x OMC
Ligand 5MC 2 x 5MC

Experiments and Validation Details

Entry percentile scores
Resolution: 2.75Å
Relevant EMDB volumes: EMD-13681

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)