8ife

Electron Microscopy
2.57Å resolution

Arbekacin-added human 80S ribosome

Released:

Function and Biology Details

Reaction catalysed:
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 80-mer (preferred)
PDBe Complex ID:
PDB-CPX-272442 (preferred)
Entry contents:
76 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (80 distinct):
Large ribosomal subunit protein uL2 Chain: 1D
Molecule details ›
Chain: 1D
Length: 257 amino acids
Theoretical weight: 28.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62917 (Residues: 1-257; Coverage: 100%)
Gene name: RPL8
Sequence domains:
Large ribosomal subunit protein uL3 Chain: 1E
Molecule details ›
Chain: 1E
Length: 403 amino acids
Theoretical weight: 46.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39023 (Residues: 1-403; Coverage: 100%)
Gene names: OK/SW-cl.32, RPL3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: 1F
Large ribosomal subunit protein uL18 Chain: 1G
Large ribosomal subunit protein eL6 Chain: 1H
Large ribosomal subunit protein uL30 Chain: 2A
Large ribosomal subunit protein eL8 Chain: 2B
Large ribosomal subunit protein uL6 Chain: 2C
Ribosomal protein uL16-like Chain: 2D
Large ribosomal subunit protein uL5 Chain: 2E
Large ribosomal subunit protein eL13 Chain: 2F
Large ribosomal subunit protein eL14 Chain: 2G
Large ribosomal subunit protein eL15 Chain: 2H
Large ribosomal subunit protein uL13 Chain: 2I
Large ribosomal subunit protein uL22 Chain: 2J
Large ribosomal subunit protein eL18 Chain: 2K
Large ribosomal subunit protein eL19 Chain: 2L
Large ribosomal subunit protein eL20 Chain: 2M
Large ribosomal subunit protein eL21 Chain: 2N
Large ribosomal subunit protein eL22 Chain: 2O
Large ribosomal subunit protein uL14 Chain: 2P
Large ribosomal subunit protein eL24 Chain: 2Q
Large ribosomal subunit protein uL23 Chain: 2R
Large ribosomal subunit protein uL24 Chain: 2S
Large ribosomal subunit protein eL27 Chain: 2T
Large ribosomal subunit protein uL15 Chain: 2U
Large ribosomal subunit protein eL29 Chain: 2V
Large ribosomal subunit protein eL30 Chain: 2W
Large ribosomal subunit protein eL31 Chain: 2X
Large ribosomal subunit protein eL32 Chain: 2Y
Large ribosomal subunit protein eL33 Chain: 2Z
Large ribosomal subunit protein eL34 Chain: 2a
Large ribosomal subunit protein uL29 Chain: 2b
Large ribosomal subunit protein eL36 Chain: 2c
Large ribosomal subunit protein eL37 Chain: 2d
Large ribosomal subunit protein eL38 Chain: 2e
Large ribosomal subunit protein eL39 Chain: 2f
Ubiquitin-ribosomal protein eL40 fusion protein Chain: 2g
Small ribosomal subunit protein eS32 Chain: 2h
Large ribosomal subunit protein eL42 Chain: 2i
Large ribosomal subunit protein eL43 Chain: 2j
Large ribosomal subunit protein eL28 Chain: 2k
Large ribosomal subunit protein uL1 Chain: 2l
Small ribosomal subunit protein uS2 Chain: 2n
Small ribosomal subunit protein eS1 Chain: 2o
Small ribosomal subunit protein uS3 Chain: 2p
Small ribosomal subunit protein eS4, X isoform Chain: 2q
Small ribosomal subunit protein uS7 Chain: 2r
Small ribosomal subunit protein eS7 Chain: 2s
Small ribosomal subunit protein eS8 Chain: 2t
Small ribosomal subunit protein eS10 Chain: 2u
Small ribosomal subunit protein uS17 Chain: 2v
Small ribosomal subunit protein uS19 Chain: 2w
Small ribosomal subunit protein uS9 Chain: 2x
Small ribosomal subunit protein eS17 Chain: 2y
Small ribosomal subunit protein uS13 Chain: 2z
Small ribosomal subunit protein eS19 Chain: 20
Small ribosomal subunit protein uS10 Chain: 21
Small ribosomal subunit protein eS21 Chain: 3A
Small ribosomal subunit protein uS12 Chain: 3B
Small ribosomal subunit protein eS26 Chain: 3C
Small ribosomal subunit protein eS28 Chain: 3D
Small ribosomal subunit protein uS14 Chain: 3E
Small ribosomal subunit protein RACK1 Chain: 3F
Small ribosomal subunit protein uS5 Chain: 3G
Small ribosomal subunit protein eS6 Chain: 3H
Small ribosomal subunit protein uS4 Chain: 3I
Small ribosomal subunit protein eS12 Chain: 3J
Small ribosomal subunit protein uS15 Chain: 3K
Small ribosomal subunit protein uS11 Chain: 3L
Small ribosomal subunit protein uS8 Chain: 3M
Small ribosomal subunit protein eS24 Chain: 3N
Small ribosomal subunit protein eS25 Chain: 3O
Small ribosomal subunit protein eS27 Chain: 3P
Small ribosomal subunit protein eS30 Chain: 3Q
Ubiquitin-ribosomal protein eS31 fusion protein Chain: 3R
28S ribosomal RNA Chain: 1A
5S ribosomal RNA Chain: 1B
5.8S ribosomal RNA Chain: 1C
18S Ribosomal RNA Chain: 2m

Ligands and Environments

3 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
Resolution: 2.57Å
Relevant EMDB volumes: EMD-35414