› 9b0h

Electron Microscopy
2.59Å resolution

In situ human Hibernating class5 80S ribosome

Released:
DOI: 10.2210/pdb9b0h/pdb
PDB entry 9b0h coloured by chain, front view.
PDB entry 9b0h coloured by chain, side view.
PDB entry 9b0h coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Wei Z, Yong X
Related structures: EMD-44041

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

Structure analysis Details

Assembly composition:
hetero 85-mer (preferred)
PDBe Complex ID:
PDB-CPX-292336 (preferred)
Entry contents:
80 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (85 distinct):
Large ribosomal subunit protein uL2 Chain: LA
Molecule details ›
Chain: LA
Length: 248 amino acids
Theoretical weight: 27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62917 (Residues: 2-249; Coverage: 97%)
Gene name: RPL8
Sequence domains:
Large ribosomal subunit protein uL3 Chain: LB
Molecule details ›
Chain: LB
Length: 402 amino acids
Theoretical weight: 46.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39023 (Residues: 2-403; Coverage: 100%)
Gene names: OK/SW-cl.32, RPL3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: LC
Large ribosomal subunit protein uL18 Chain: LD
Large ribosomal subunit protein eL6 Chain: LE
Large ribosomal subunit protein uL30 Chain: LF
Large ribosomal subunit protein eL8 Chain: LG
Large ribosomal subunit protein uL6 Chain: LH
Ribosomal protein uL16-like Chain: LI
Large ribosomal subunit protein uL5 Chain: LJ
Large ribosomal subunit protein eL13 Chain: LL
Large ribosomal subunit protein eL14 Chain: LM
Large ribosomal subunit protein eL15 Chain: LN
Large ribosomal subunit protein uL13 Chain: LO
Large ribosomal subunit protein uL22 Chain: LP
Large ribosomal subunit protein eL18 Chain: LQ
Large ribosomal subunit protein eL19 Chain: LR
Large ribosomal subunit protein eL20 Chain: LS
Large ribosomal subunit protein eL21 Chain: LT
Large ribosomal subunit protein eL22 Chain: LU
Large ribosomal subunit protein uL14 Chain: LV
Large ribosomal subunit protein uL23 Chain: LX
Large ribosomal subunit protein uL24 Chain: LY
Large ribosomal subunit protein eL27 Chain: LZ
Large ribosomal subunit protein uL15 Chain: La
Large ribosomal subunit protein eL29 Chain: Lb
Large ribosomal subunit protein eL30 Chain: Lc
Large ribosomal subunit protein eL31 Chain: Ld
Large ribosomal subunit protein eL32 Chain: Le
Large ribosomal subunit protein eL33 Chain: Lf
Large ribosomal subunit protein eL34 Chain: Lg
Large ribosomal subunit protein uL29 Chain: Lh
Large ribosomal subunit protein eL36 Chain: Li
Large ribosomal subunit protein eL37 Chain: Lj
Large ribosomal subunit protein eL38 Chain: Lk
Large ribosomal subunit protein eL39 Chain: Ll
Large ribosomal subunit protein eL40 Chain: Lm
Small ribosomal subunit protein eS32 Chain: Ln
Large ribosomal subunit protein eL42 Chain: Lo
Large ribosomal subunit protein eL43 Chain: Lp
Large ribosomal subunit protein eL28 Chain: Lr
Large ribosomal subunit protein uL1 Chain: Lz
Proliferation-associated protein 2G4 Chain: CA
Large ribosomal subunit protein uL10 Chain: Ls
60S ribosomal protein L12 [Homo sapiens] Chain: Lt
Small ribosomal subunit protein uS3 Chain: SD
Small ribosomal subunit protein uS7 Chain: SF
Small ribosomal subunit protein eS10 Chain: SK
Small ribosomal subunit protein uS19 Chain: SP
Small ribosomal subunit protein uS9 Chain: SQ
Small ribosomal subunit protein uS13 Chain: SS
Small ribosomal subunit protein eS19 Chain: ST
Small ribosomal subunit protein uS10 Chain: SU
Small ribosomal subunit protein eS28 Chain: Sc
Small ribosomal subunit protein uS14 Chain: Sd
Small ribosomal subunit protein RACK1 Chain: Sg
Small ribosomal subunit protein eS12 Chain: SM
Small ribosomal subunit protein eS25 Chain: SZ
Small ribosomal subunit protein eS31 Chain: Sf
Serbp1 Chain: CD
Large ribosomal subunit protein eL24 Chain: LW
Small ribosomal subunit protein eS4, X isoform Chain: SE
Small ribosomal subunit protein eS8 Chain: SI
Small ribosomal subunit protein uS17 Chain: SL
Small ribosomal subunit protein uS12 Chain: SX
Small ribosomal subunit protein eS6 Chain: SG
Small ribosomal subunit protein uS4 Chain: SJ
Small ribosomal subunit protein eS24 Chain: SY
Small ribosomal subunit protein eS30 Chain: Se
Small ribosomal subunit protein uS2 Chain: SA
Small ribosomal subunit protein eS1 Chain: SB
Small ribosomal subunit protein eS7 Chain: SH
Small ribosomal subunit protein eS21 Chain: SV
Small ribosomal subunit protein eS26 Chain: Sa
Small ribosomal subunit protein uS5 Chain: SC
Small ribosomal subunit protein uS15 Chain: SN
Small ribosomal subunit protein uS11 Chain: SO
Small ribosomal subunit protein uS8 Chain: SW
Small ribosomal subunit protein eS27 Chain: Sb
Elongation factor 2 Chain: CB
18S Ribosomal RNA Chain: S2
28S ribosomal RNA Chain: L5
5S ribosomal RNA Chain: L7
5.8S ribosomal RNA Chain: L8
E site tRNA [Homo sapiens] Chain: Et

Ligands and Environments

2 bound ligands:
Ligand MG 255 x MG
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 2.59Å
Relevant EMDB volumes: EMD-44041

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