› 5t2c

Electron Microscopy
3.6Å resolution

CryoEM structure of the human ribosome at 3.6 Angstrom resolution

Released:
DOI: 10.2210/pdb5t2c/pdb
PDB entry 5t2c coloured by chain, front view.
PDB entry 5t2c coloured by chain, side view.
PDB entry 5t2c coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures and stabilization of kinetoplastid-specific split rRNAs revealed by comparing leishmanial and human ribosomes.
Zhang X, Lai M, Chang W, Yu I, Ding K, Mrazek J, Ng HL, Yang OO, Maslov DA, Zhou ZH
OpenAccess logo Nat Commun 7 13223 (2016)
PMID: 27752045
Related structures: EMD-8345

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 81-mer (preferred)
PDBe Complex ID:
PDB-CPX-289711 (preferred)
Entry contents:
76 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (81 distinct):
Large ribosomal subunit protein uL2 Chain: D
Molecule details ›
Chain: D
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: E
Molecule details ›
Chain: E
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: F
Large ribosomal subunit protein uL18 Chain: G
Large ribosomal subunit protein uL13 Chain: I
Large ribosomal subunit protein uL22 Chain: J
Large ribosomal subunit protein eL19 Chain: L
Large ribosomal subunit protein eL21 Chain: N
Large ribosomal subunit protein eL22 Chain: O
Large ribosomal subunit protein uL14 Chain: P
Large ribosomal subunit protein eL24 Chain: Q
Large ribosomal subunit protein uL24 Chain: S
Large ribosomal subunit protein eL27 Chain: T
Large ribosomal subunit protein uL15 Chain: U
Large ribosomal subunit protein eL29 Chain: V
Large ribosomal subunit protein eL31 Chain: X
Large ribosomal subunit protein eL32 Chain: Y
Large ribosomal subunit protein eL33 Chain: Z
Large ribosomal subunit protein eL34 Chain: a
Large ribosomal subunit protein uL29 Chain: b
Large ribosomal subunit protein eL36 Chain: c
Large ribosomal subunit protein eL37 Chain: d
Large ribosomal subunit protein eL38 Chain: e
Large ribosomal subunit protein eL39 Chain: f
Ubiquitin-ribosomal protein eL40 fusion protein Chain: g
Large ribosomal subunit protein eL43 Chain: j
Large ribosomal subunit protein eL28 Chain: k
Large ribosomal subunit protein uL30 Chain: m
Large ribosomal subunit protein eL8 Chain: n
Large ribosomal subunit protein uL6 Chain: o
Large ribosomal subunit protein eL14 Chain: s
Large ribosomal subunit protein eL15 Chain: t
60S Ribosomal protein L41 Chain: h
Large ribosomal subunit protein eL13 Chain: r
Large ribosomal subunit protein eL6 Chain: H
Large ribosomal subunit protein eL42 Chain: i
Large ribosomal subunit protein eL18 Chain: K
Large ribosomal subunit protein uL1 Chain: l
Large ribosomal subunit protein eL20 Chain: M
Ribosomal protein uL16-like Chain: p
Large ribosomal subunit protein uL5 Chain: q
Large ribosomal subunit protein uL23 Chain: R
Large ribosomal subunit protein eL30 Chain: W
Small ribosomal subunit protein eS21 Chain: AC
Small ribosomal subunit protein uS12 Chain: AD
Small ribosomal subunit protein eS26 Chain: AE
Small ribosomal subunit protein eS28 Chain: AF
Ubiquitin-ribosomal protein eS31 fusion protein Chain: AH
Small ribosomal subunit protein uS5 Chain: AJ
Small ribosomal subunit protein eS6 Chain: AK
Small ribosomal subunit protein uS4 Chain: AL
Small ribosomal subunit protein uS15 Chain: AN
Small ribosomal subunit protein uS8 Chain: AP
Small ribosomal subunit protein eS24 Chain: AQ
Small ribosomal subunit protein eS25 Chain: AR
Small ribosomal subunit protein eS30 Chain: AT
Small ribosomal subunit protein eS27 Chain: AV
Small ribosomal subunit protein eS1 Chain: Ap
Small ribosomal subunit protein uS3 Chain: Aq
Small ribosomal subunit protein eS4, X isoform Chain: Ar
Small ribosomal subunit protein eS7 Chain: At
Small ribosomal subunit protein eS8 Chain: Au
Small ribosomal subunit protein eS10 Chain: Av
Small ribosomal subunit protein uS9 Chain: Ay
Small ribosomal subunit protein uS13 Chain: A0
Small ribosomal subunit protein uS2 Chain: Ao
Small ribosomal subunit protein uS7 Chain: As
Small ribosomal subunit protein uS17 Chain: Aw
Small ribosomal subunit protein uS19 Chain: Ax
Small ribosomal subunit protein eS17 Chain: Az
Small ribosomal subunit protein uS10 Chain: AB
Small ribosomal subunit protein uS14 Chain: AG
Small ribosomal subunit protein RACK1 Chain: AI
Small ribosomal subunit protein eS12 Chain: AM
Small ribosomal subunit protein uS11 Chain: AO
Small ribosomal subunit protein eS19 Chain: AU
5S ribosomal RNA Chain: B
5.8S ribosomal RNA Chain: C
28S ribosomal RNA Chain: A
18S Ribosomal RNA Chain: AA
tRNA Chain: An

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.6Å
Relevant EMDB volumes: EMD-8345

Quick links

Citations

7 review citations

New Insights into Ribosome Structure and Function.
Jobe et al. (2019)
6 more

13 mentions without citation

Ribosome Stoichiometry: From Form to Function.
Emmott et al. (2019)
12 more