5AJ3 image
Deposition Date 2015-02-20
Release Date 2015-04-22
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5AJ3
Keywords:
RIBOSOME
Title:
Structure of the small subunit of the mammalian mitoribosome
Biological Source:
Source Organism(s):
Sus scrofa (Taxon ID: 9823)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5AJ3 validation report missing
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:MITORIBOSOMAL 12S RRNA
Chain IDs:A
Chain Length:360
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US2M, M
Gene (Uniprot):MRPS2
Chain IDs:B
Chain Length:289
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1S001 Pfam ID:PF00318
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US3M, M
Gene (Uniprot):MRPS24
Chain IDs:C
Chain Length:173
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1ST79 Pfam ID:PF14955
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US5M, M
Gene (Uniprot):MRPS5
Chain IDs:D (auth: E)
Chain Length:336
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SU66 Pfam ID:PF21251, PF00333, PF03719
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN BS6M, M
Chain IDs:E (auth: F)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US7M, M
Chain IDs:F (auth: G)
Chain Length:397
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US9M, M
Chain IDs:G (auth: I)
Chain Length:106
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A0M3KL59 Pfam ID:PF00380
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US10M,
Chain IDs:H (auth: J)
Chain Length:218
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RUU2 Pfam ID:PF00338
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US11M,
Chain IDs:I (auth: K)
Chain Length:196
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US12M,
Chain IDs:J (auth: L)
Chain Length:139
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A0M3KL52 Pfam ID:PF00164
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US14M,
Chain IDs:K (auth: N)
Chain Length:199
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A0M3KL53 Pfam ID:PF00253
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US15M,
Chain IDs:L (auth: O)
Chain Length:239
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN BS16M,
Chain IDs:M (auth: P)
Chain Length:135
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN US17M,
Chain IDs:N (auth: Q)
Chain Length:130
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D1UDM1 Pfam ID:PF00366
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN BS18M,
Chain IDs:O (auth: R)
Chain Length:143
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A0M3KL54 Pfam ID:PF01084
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN BL19M,
Chain IDs:P (auth: T)
Chain Length:14
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN BS21M,
Chain IDs:Q (auth: U)
Chain Length:87
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polyribonucleotide
Molecule:P-SITE AND A-SITE TRNA
Chain IDs:R (auth: V), T (auth: Y)
Chain Length:64
Number of Molecules:2
Biological Source:Sus scrofa
Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:S (auth: X)
Chain Length:13
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS22, M
Chain IDs:U (auth: a)
Chain Length:360
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS23, M
Chain IDs:V (auth: b)
Chain Length:289
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS25, M
Chain IDs:W (auth: c)
Chain Length:173
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A0M3KL55 Pfam ID:PF05047
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS26, M
Gene (Uniprot):MRPS26
Chain IDs:X (auth: d)
Chain Length:205
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1S8A5 Pfam ID:PF14943
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS27, M
Chain IDs:Y (auth: e)
Chain Length:336
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS28, M
Chain IDs:Z (auth: f)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A0M3KL56 Pfam ID:PF10246
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS29, M
Chain IDs:AA (auth: g)
Chain Length:397
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RLM4 Pfam ID:PF10236
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS31, M
Gene (Uniprot):MRPS31
Chain IDs:BA (auth: h)
Chain Length:387
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RME2 Pfam ID:PF15433
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS33, M
Chain IDs:CA (auth: i)
Chain Length:106
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1V2H3 Pfam ID:PF08293
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS34, M
Chain IDs:DA (auth: j)
Chain Length:218
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS35, M
Gene (Uniprot):MRPS35
Chain IDs:EA (auth: k)
Chain Length:196
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1SG95 Pfam ID:PF10213
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS37, M
Chain IDs:FA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1SZV4 Pfam ID:PF06747
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS38, M
Chain IDs:GA (auth: n)
Chain Length:199
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A0M3KL57 Pfam ID:PF08213
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS39, M
Gene (Uniprot):PTCD3
Chain IDs:HA (auth: o)
Chain Length:239
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:K7GKS8 Pfam ID:PF22330, PF13812
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MITORIBOSOMAL PROTEIN MS40, M
Gene (Uniprot):MRPS18B
Chain IDs:IA (auth: p)
Chain Length:135
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:Q767K8 Pfam ID:PF01084
Polymer Type:polypeptide(L)
Molecule:UNASSIGNED HELICES
Chain IDs:JA (auth: s)
Chain Length:16
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:UNASSIGNED HELICES
Chain IDs:KA (auth: z)
Chain Length:17
Number of Molecules:1
Biological Source:Sus scrofa
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
P5P R A PURINE RIBOSIDE-5'-MONOPHOSPHATE
Ligand Molecules
GDP
MG
ZN
Primary Citation
Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome.
Science 348 303 308 (2015)
PMID: 25837512 DOI: 10.1126/science.aaa3872

Abstact

Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of the porcine 55S mitoribosome at 3.8 angstrom resolution by cryo-electron microscopy and chemical cross-linking/mass spectrometry. The structure of the 28S subunit in the complex was resolved at 3.6 angstrom resolution by focused alignment, which allowed building of a detailed atomic structure including all of its 15 mitoribosomal-specific proteins. The structure reveals the intersubunit contacts in the 55S mitoribosome, the molecular architecture of the mitoribosomal messenger RNA (mRNA) binding channel and its interaction with transfer RNAs, and provides insight into the highly specialized mechanism of mRNA recruitment to the 28S subunit. Furthermore, the structure contributes to a mechanistic understanding of aminoglycoside ototoxicity.

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Protein

Chemical

Disease

Primary Citation of related structures
5AJ4
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