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PDBsum entry 4ce4
Go to PDB code: 
protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
4ce4

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
76 a.a.
58 a.a.
76 a.a.
59 a.a.
68 a.a.
48 a.a.
43 a.a.
60 a.a.
36 a.a.
200 a.a.
208 a.a.
224 a.a.
57 a.a.
147 a.a.
114 a.a.
169 a.a.
154 a.a.
120 a.a.
94 a.a.
119 a.a.
123 a.a.
109 a.a.
134 a.a.
87 a.a.
103 a.a.
192 a.a.
292 a.a.
272 a.a.
161 a.a.
76 a.a.
56 a.a.
90 a.a.
426 a.a.
DNA/RNA
Ligands
__N-__N-__N-__N-
__N-__N-__N-__N-
__N-__N-__N-__N-
__N-__N-__N-__N-
__N-__N-__N-__N-
__N-__N
__N-__N-__N-__N-
__N-__N-__N
Metals
_ZN ×2
PDB id:
4ce4
Name: Ribosome
Title: 39s large subunit of the porcine mitochondrial ribosome
Structure: Mrpl27. Chain: 0. Mrpl28. Chain: 1. Mrpl47. Chain: 2. Mrpl30. Chain: 3. Mrpl32.
Source: Sus scrofa domestica. Domestic pig. Organism_taxid: 9825. Organ: liver. Organelle: mitochondria. Organelle: mitochondria
Authors: B.J.Greber,D.Boehringer,A.Leitner,P.Bieri,F.Voigts-Hoffmann, J.P.Erzberger,M.Leibundgut,R.Aebersold,N.Ban
Key ref: B.J.Greber et al. (2014). Architecture of the large subunit of the mammalian mitochondrial ribosome. Nature, 505, 515-519. PubMed id: 24362565 DOI: 10.1038/nature12890
Date:
08-Nov-13     Release date:   18-Dec-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
A0A4X1U0F6  (A0A4X1U0F6_PIG) -  39S ribosomal protein L27, mitochondrial from Sus scrofa
Seq:
Struc: 		148 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
A0A0R4J8D5  (A0A0R4J8D5_PIG) -  39S ribosomal protein L18, mitochondrial isoform 1 from Sus scrofa
Seq:
Struc: 		180 a.a.
58 a.a.*
Protein chain
Pfam   ArchSchema ?
F1SGC7  (F1SGC7_PIG) -  Large ribosomal subunit protein uL29m from Sus scrofa
Seq:
Struc: 		250 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
A0A8D1MIP3  (A0A8D1MIP3_PIG) -  Large ribosomal subunit protein uL30m from Sus scrofa
Seq:
Struc: 		161 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
I3LTC4  (I3LTC4_PIG) -  Large ribosomal subunit protein bL32m from Sus scrofa
Seq:
Struc: 		207 a.a.
68 a.a.*
Protein chain
No UniProt id for this chain
Struc: 48 a.a.
Protein chain
Pfam   ArchSchema ?
W5IDC1  (W5IDC1_PIG) -  Large ribosomal subunit protein bL34m from Sus scrofa domesticus
Seq:
Struc: 		95 a.a.
43 a.a.
Protein chain
F1SVC5  (F1SVC5_PIG) -  Large ribosomal subunit protein bL35m from Sus scrofa
Seq:
Struc: 		95 a.a.
60 a.a.*
Protein chain
No UniProt id for this chain
Struc: 36 a.a.
Protein chain
Pfam   ArchSchema ?
F1RRN2  (F1RRN2_PIG) -  Mitochondrial ribosomal protein L2 from Sus scrofa
Seq:
Struc: 		226 a.a.
200 a.a.*
Protein chain
No UniProt id for this chain
Struc: 208 a.a.
Protein chain
No UniProt id for this chain
Struc: 224 a.a.
Protein chain
Pfam   ArchSchema ?
I3LR45  (I3LR45_PIG) -  Large ribosomal subunit protein bL9m from Sus scrofa
Seq:
Struc: 		268 a.a.
57 a.a.
Protein chain
No UniProt id for this chain
Struc: 147 a.a.
Protein chain
Pfam   ArchSchema ?
F1RQV7  (F1RQV7_PIG) -  Large ribosomal subunit protein uL14m from Sus scrofa
Seq:
Struc: 		193 a.a.
114 a.a.
Protein chain
No UniProt id for this chain
Struc: 169 a.a.
Protein chain
Pfam   ArchSchema ?
F1RI89  (F1RI89_PIG) -  Large ribosomal subunit protein uL16m from Sus scrofa
Seq:
Struc: 		251 a.a.
154 a.a.*
Protein chain
Pfam   ArchSchema ?
F1RMQ4  (F1RMQ4_PIG) -  Large ribosomal subunit protein bL17m from Sus scrofa
Seq:
Struc: 		169 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
A0A0R4J8D5  (A0A0R4J8D5_PIG) -  39S ribosomal protein L18, mitochondrial isoform 1 from Sus scrofa
Seq:
Struc: 		180 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
I3LNJ0  (I3LNJ0_PIG) -  Large ribosomal subunit protein bL19m from Sus scrofa
Seq:
Struc: 		303 a.a.
119 a.a.
Protein chain
No UniProt id for this chain
Struc: 123 a.a.
Protein chain
Pfam   ArchSchema ?
F1RY70  (F1RY70_PIG) -  Large ribosomal subunit protein bL21m from Sus scrofa
Seq:
Struc: 		209 a.a.
109 a.a.*
Protein chain
Pfam   ArchSchema ?
W5IDB8  (W5IDB8_PIG) -  Large ribosomal subunit protein uL22m from Sus scrofa domesticus
Seq:
Struc: 		134 a.a.
134 a.a.
Protein chains
Pfam   ArchSchema ?
W5IDB9  (W5IDB9_PIG) -  Large ribosomal subunit protein uL23m from Sus scrofa domesticus
Seq:
Struc: 		87 a.a.
87 a.a.
Protein chain
Pfam   ArchSchema ?
F1RHJ1  (F1RHJ1_PIG) -  Large ribosomal subunit protein uL24m from Sus scrofa
Seq:
Struc: 		216 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
F1RW03  (F1RW03_PIG) -  Large ribosomal subunit protein mL38 from Sus scrofa
Seq:
Struc: 		380 a.a.
192 a.a.
Protein chain
Pfam   ArchSchema ?
F1SHP6  (F1SHP6_PIG) -  Mitochondrial ribosomal protein L39 from Sus scrofa
Seq:
Struc: 		318 a.a.
292 a.a.*
Protein chain
Pfam   ArchSchema ?
F1SR64  (F1SR64_PIG) -  Large ribosomal subunit protein mL44 from Sus scrofa
Seq:
Struc: 		332 a.a.
272 a.a.*
Protein chain
Pfam   ArchSchema ?
I3LGM5  (I3LGM5_PIG) -  Large ribosomal subunit protein mL45 from Sus scrofa
Seq:
Struc: 		306 a.a.
161 a.a.
Protein chain
Pfam   ArchSchema ?
A0A0R4J8D5  (A0A0R4J8D5_PIG) -  39S ribosomal protein L18, mitochondrial isoform 1 from Sus scrofa
Seq:
Struc: 		180 a.a.
76 a.a.*
Protein chain
No UniProt id for this chain
Struc: 56 a.a.
Protein chain
Pfam   ArchSchema ?
W5IDC0  (W5IDC0_PIG) -  Large ribosomal subunit protein mL62 from Sus scrofa domesticus
Seq:
Struc: 		205 a.a.
90 a.a.
Protein chain
No UniProt id for this chain
Struc: 426 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 281 residue positions (black crosses)

DNA/RNA chain
  A-C-C-A-A-A-G-C-U-A-G-C-U-C-A-A-C-A-U-__N-__N-__N-__N-__N-__N-__N-A-A-A-U-A-A- ... 1444 bases

 Enzyme reactions 
   Enzyme class: Chain u: E.C.3.1.1.29  - peptidyl-tRNA hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: an N-acyl-L-alpha-aminoacyl-tRNA + H2O = an N-acyl-L-amino acid + a tRNA + H+
N-acyl-L-alpha-aminoacyl-tRNA
 + H2O
 = N-acyl-L-amino acid
 + tRNA
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1038/nature12890 Nature 505:515-519 (2014)
PubMed id: 24362565  
 
 
Architecture of the large subunit of the mammalian mitochondrial ribosome.
B.J.Greber, D.Boehringer, A.Leitner, P.Bieri, F.Voigts-Hoffmann, J.P.Erzberger, M.Leibundgut, R.Aebersold, N.Ban.
 
  ABSTRACT  
 
Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain.
 

 

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