› 4ce4

Electron Microscopy
4.9Å resolution

39S large subunit of the porcine mitochondrial ribosome

Released:
DOI: 10.2210/pdb4ce4/pdb
PDB entry 4ce4 coloured by chain, front view.
PDB entry 4ce4 coloured by chain, side view.
PDB entry 4ce4 coloured by chain, top view.
Source organism: Sus scrofa domesticus
Primary publication:
Architecture of the large subunit of the mammalian mitochondrial ribosome.
Greber BJ, Boehringer D, Leitner A, Bieri P, Voigts-Hoffmann F, Erzberger JP, Leibundgut M, Aebersold R, Ban N
Nature 505 515-9 (2014)
PMID: 24362565
Related structures: EMD-2490

Function and Biology Details

Reaction catalysed: 
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
PDBe Complex ID:
PDB-CPX-236645 (preferred)
Entry contents:
35 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (37 distinct):
39S ribosomal protein L27, mitochondrial Chain: 0
Molecule details ›
Chain: 0
Length: 148 amino acids
Theoretical weight: 15.94 KDa
Source organism: Sus scrofa domesticus
39S ribosomal protein L18, mitochondrial isoform 1 Chain: 1
Molecule details ›
Chain: 1
Length: 256 amino acids
Theoretical weight: 30.15 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein uL29m Chain: 2
Molecule details ›
Chain: 2
Length: 252 amino acids
Theoretical weight: 30.09 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein uL30m Chain: 3
Molecule details ›
Chain: 3
Length: 161 amino acids
Theoretical weight: 18.59 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein bL32m Chain: 5
Molecule details ›
Chain: 5
Length: 146 amino acids
Theoretical weight: 15.93 KDa
Source organism: Sus scrofa domesticus
MRPL33 Chain: 6
Molecule details ›
Chain: 6
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein bL34m Chain: 7
Molecule details ›
Chain: 7
Length: 95 amino acids
Theoretical weight: 10.87 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein bL35m Chain: 8
Molecule details ›
Chain: 8
Length: 188 amino acids
Theoretical weight: 21.55 KDa
Source organism: Sus scrofa domesticus
MRPL36 Chain: 9
Molecule details ›
Chain: 9
Length: 100 amino acids
Theoretical weight: 10.84 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein uL2 RNA-binding domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 306 amino acids
Theoretical weight: 33.27 KDa
Source organism: Sus scrofa domesticus
MRPL3 Chain: E
Molecule details ›
Chain: E
Length: 399 amino acids
Theoretical weight: 43.71 KDa
Source organism: Sus scrofa domesticus
MRPL4 Chain: F
Molecule details ›
Chain: F
Length: 224 amino acids
Theoretical weight: 24.31 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein bL9m Chain: I
Molecule details ›
Chain: I
Length: 268 amino acids
Theoretical weight: 30.37 KDa
Source organism: Sus scrofa domesticus
MRPL13 Chain: N
Molecule details ›
Chain: N
Length: 178 amino acids
Theoretical weight: 20.63 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein uL14m Chain: O
Molecule details ›
Chain: O
Length: 145 amino acids
Theoretical weight: 15.96 KDa
Source organism: Sus scrofa domesticus
MRPL15 Chain: P
Molecule details ›
Chain: P
Length: 288 amino acids
Theoretical weight: 32.47 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein uL16m Chain: Q
Molecule details ›
Chain: Q
Length: 208 amino acids
Theoretical weight: 22.75 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein bL17m Chain: R
Molecule details ›
Chain: R
Length: 169 amino acids
Theoretical weight: 19.27 KDa
Source organism: Sus scrofa domesticus
39S ribosomal protein L18, mitochondrial isoform 1 Chain: S
Molecule details ›
Chain: S
Length: 180 amino acids
Theoretical weight: 20.58 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein bL19m Chain: T
Molecule details ›
Chain: T
Length: 292 amino acids
Theoretical weight: 33.44 KDa
Source organism: Sus scrofa domesticus
MRPL20 Chain: U
Molecule details ›
Chain: U
Length: 132 amino acids
Theoretical weight: 15.56 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein bL21m Chain: V
Molecule details ›
Chain: V
Length: 207 amino acids
Theoretical weight: 22.89 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein uL22m Chain: W
Molecule details ›
Chain: W
Length: 134 amino acids
Theoretical weight: 15.07 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein uL23m Chain: X
Molecule details ›
Chain: X
Length: 87 amino acids
Theoretical weight: 9.81 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein uL24m Chain: Y
Molecule details ›
Chain: Y
Length: 216 amino acids
Theoretical weight: 24.89 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein mL38 Chain: b
Molecule details ›
Chain: b
Length: 380 amino acids
Theoretical weight: 44.66 KDa
Source organism: Sus scrofa domesticus
TGS domain-containing protein Chain: c
Molecule details ›
Chain: c
Length: 301 amino acids
Theoretical weight: 33.83 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein mL44 Chain: h
Molecule details ›
Chain: h
Length: 298 amino acids
Theoretical weight: 32.64 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein mL45 Chain: i
Molecule details ›
Chain: i
Length: 312 amino acids
Theoretical weight: 36.12 KDa
Source organism: Sus scrofa domesticus
39S ribosomal protein L18, mitochondrial isoform 1 Chain: l
Molecule details ›
Chain: l
Length: 166 amino acids
Theoretical weight: 18.96 KDa
Source organism: Sus scrofa domesticus
MRPL52 Chain: o
Molecule details ›
Chain: o
Length: 56 amino acids
Theoretical weight: 4.78 KDa
Source organism: Sus scrofa domesticus
Large ribosomal subunit protein mL62 Chain: u
Molecule details ›
Chain: u
Length: 205 amino acids
Theoretical weight: 23.55 KDa
Source organism: Sus scrofa domesticus
UNASSIGNED HELICES Chains: v, w
Molecule details ›
Chains: v, w
Length: 91 amino acids
Theoretical weight: 7.76 KDa
Source organism: Sus scrofa domesticus
THIOREDOXIN FOLD Chain: x
Molecule details ›
Chain: x
Length: 85 amino acids
Theoretical weight: 7.25 KDa
Source organism: Sus scrofa domesticus
UNASSIGNED HELICES Chain: z
Molecule details ›
Chain: z
Length: 426 amino acids
Theoretical weight: 36.27 KDa
Source organism: Sus scrofa domesticus
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1570 nucleotides
Theoretical weight: 501.42 KDa
Source organism: Sus scrofa domesticus
Sequence domains: Bacterial large subunit ribosomal RNA
UNASSIGNED RNA Chain: B
Molecule details ›
Chain: B
Length: 29 nucleotides
Theoretical weight: 5.64 KDa
Source organism: Sus scrofa domesticus

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.9Å
Relevant EMDB volumes: EMD-2490

Quick links

Citations

47 review citations

Multidimensional proteomics for cell biology.
Larance et al. (2015)
46 more

7 mentions without citation

Principles for Integrative Structural Biology Studies.
Rout et al. (2019)
6 more