› 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:
Biological process:
Cellular component:
Sequence domains:

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
UniProt:
  • Canonical: A0A4X1U0F6 (Residues: 1-148; Coverage: 100%)
Gene name: MRPL27
Sequence domains: Ribosomal L27 protein
Mitochondrial ribosomal protein L18 Chain: 1
Molecule details ›
Chain: 1
Length: 256 amino acids
Theoretical weight: 30.15 KDa
Source organism: Sus scrofa domesticus
UniProt:
  • Canonical: A0A0R4J8D5 (Residues: 71-97; Coverage: 17%)
Gene name: MRPL18
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
UniProt:
  • Canonical: F1SGC7 (Residues: 1-32, 33-250; Coverage: 100%)
Gene name: MRPL47
Sequence domains: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
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
UniProt:
  • Canonical: A0A8D1MIP3 (Residues: 8-161; Coverage: 96%)
Gene name: MRPL30
Sequence domains: Ribosomal protein L30p/L7e
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
UniProt:
  • Canonical: I3LTC4 (Residues: 20-145; Coverage: 61%)
Gene name: MRPL32
Sequence domains: Ribosomal L32p protein family
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
UniProt:
  • Canonical: W5IDC1 (Residues: 1-95; Coverage: 100%)
Gene name: MRPL34
Sequence domains: Ribosomal protein L34
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
UniProt:
  • Canonical: F1SVC5 (Residues: 1-79; Coverage: 83%)
Gene name: MRPL35
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
UniProt:
  • Canonical: F1RRN2 (Residues: 1-216; Coverage: 96%)
Gene name: MRPL2
Sequence domains: Ribosomal Proteins L2, RNA binding domain
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
UniProt:
  • Canonical: I3LR45 (Residues: 1-268; Coverage: 100%)
Gene name: MRPL9
Sequence domains: Ribosomal protein L9, N-terminal domain
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
UniProt:
  • Canonical: F1RQV7 (Residues: 49-193; Coverage: 75%)
Gene name: MRPL14
Sequence domains: Ribosomal protein L14p/L23e
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
UniProt:
  • Canonical: F1RI89 (Residues: 1-191; Coverage: 76%)
Gene name: MRPL16
Sequence domains: Ribosomal protein L16p/L10e
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
UniProt:
  • Canonical: F1RMQ4 (Residues: 1-169; Coverage: 100%)
Gene name: MRPL17
Sequence domains: Ribosomal protein L17
Mitochondrial ribosomal protein L18 Chain: S
Molecule details ›
Chain: S
Length: 180 amino acids
Theoretical weight: 20.58 KDa
Source organism: Sus scrofa domesticus
UniProt:
  • Canonical: A0A0R4J8D5 (Residues: 1-180; Coverage: 100%)
Gene name: MRPL18
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
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
UniProt:
  • Canonical: I3LNJ0 (Residues: 12-303; Coverage: 96%)
Gene name: MRPL19
Sequence domains: Ribosomal protein L19
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
UniProt:
  • Canonical: F1RY70 (Residues: 1-203; Coverage: 97%)
Sequence domains: Ribosomal prokaryotic L21 protein
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
UniProt:
  • Canonical: W5IDB8 (Residues: 1-110; Coverage: 82%)
Sequence domains: Ribosomal protein L22p/L17e
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
UniProt:
  • Canonical: W5IDB9 (Residues: 15-82; Coverage: 78%)
Sequence domains: Ribosomal protein L23
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
UniProt:
  • Canonical: F1RHJ1 (Residues: 1-216; Coverage: 100%)
Gene name: MRPL24
Sequence domains:
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
UniProt:
  • Canonical: F1RW03 (Residues: 1-380; Coverage: 100%)
Gene name: MRPL38
Sequence domains: Phosphatidylethanolamine-binding protein
TGS domain-containing protein Chain: c
Molecule details ›
Chain: c
Length: 301 amino acids
Theoretical weight: 33.83 KDa
Source organism: Sus scrofa domesticus
UniProt:
  • Canonical: F1SHP6 (Residues: 66-303, 304-318; Coverage: 80%)
Gene name: MRPL39
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
UniProt:
  • Canonical: F1SR64 (Residues: 67-332; Coverage: 80%)
Gene name: MRPL44
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
UniProt:
  • Canonical: I3LGM5 (Residues: 1-306; Coverage: 100%)
Gene name: MRPL45
Sequence domains: Tim44-like domain
Mitochondrial ribosomal protein L18 Chain: l
Molecule details ›
Chain: l
Length: 166 amino acids
Theoretical weight: 18.96 KDa
Source organism: Sus scrofa domesticus
UniProt:
  • Canonical: A0A0R4J8D5 (Residues: 146-150, 151-163; Coverage: 11%)
Gene name: MRPL18
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
UniProt:
  • Canonical: W5IDC0 (Residues: 1-205; Coverage: 100%)
Sequence domains: RF-1 domain
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
Sequence domains: Bacterial large subunit ribosomal RNA
UNASSIGNED RNA Chain: B
Molecule details ›
Chain: B
Length: 29 nucleotides
Theoretical weight: 5.64 KDa

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

45 review citations

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

7 mentions without citation

'Black sheep' that don't leave the double-stranded RNA-binding domain fold.
Gleghorn et al. (2014)
6 more