7PNY image
Deposition Date 2021-09-08
Release Date 2022-06-15
Last Version Date 2024-04-24
Entry Detail
PDB ID:
7PNY
Keywords:
RIBOSOME
Title:
Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation b
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.06 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7PNY validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S34, mitochondrial
Gene (Uniprot):MRPS34
Chain IDs:AA (auth: 0)
Chain Length:218
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82930 Pfam ID:PF16053
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S35, mitochondrial
Gene (Uniprot):MRPS35
Chain IDs:BA (auth: 1)
Chain Length:323
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82673 Pfam ID:PF10213
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Aurora kinase A-interacting protein
Gene (Uniprot):AURKAIP1
Chain IDs:CA (auth: 3)
Chain Length:199
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NWT8 Pfam ID:PF08213
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pentatricopeptide repeat domain-containing protein 3, mitochondrial
Gene (Uniprot):PTCD3
Chain IDs:DA (auth: 4)
Chain Length:689
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EY7 Pfam ID:PF22330, PF13812
Polymer Type:polyribonucleotide
Molecule:12S mitochondrial rRNA
Chain IDs:A
Chain Length:343
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S2, mitochondrial
Gene (Uniprot):MRPS2
Chain IDs:B
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y399 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S24, mitochondrial
Gene (Uniprot):MRPS24
Chain IDs:C
Chain Length:167
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EL2 Pfam ID:PF14955
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S5, mitochondrial
Gene (Uniprot):MRPS5
Chain IDs:D
Chain Length:430
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82675 Pfam ID:PF21251, PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S6, mitochondrial
Gene (Uniprot):MRPS6
Chain IDs:E
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82932 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S7, mitochondrial
Gene (Uniprot):MRPS7
Chain IDs:F
Chain Length:242
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y2R9 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S9, mitochondrial
Gene (Uniprot):MRPS9
Chain IDs:G
Chain Length:396
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82933 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S10, mitochondrial
Gene (Uniprot):MRPS10
Chain IDs:H
Chain Length:201
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82664 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S11, mitochondrial
Gene (Uniprot):MRPS11
Chain IDs:I
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82912 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S12, mitochondrial
Gene (Uniprot):MRPS12
Chain IDs:J
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15235 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S14, mitochondrial
Gene (Uniprot):MRPS14
Chain IDs:K
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O60783 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S15, mitochondrial
Gene (Uniprot):MRPS15
Chain IDs:L
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82914 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S16, mitochondrial
Gene (Uniprot):MRPS16
Chain IDs:M
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3D3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S17, mitochondrial
Gene (Uniprot):MRPS17
Chain IDs:N
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y2R5 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S18b, mitochondrial
Gene (Uniprot):MRPS18B
Chain IDs:O
Chain Length:258
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y676 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S18c, mitochondrial
Gene (Uniprot):MRPS18C
Chain IDs:P
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3D5 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S21, mitochondrial
Gene (Uniprot):MRPS21
Chain IDs:Q
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82921 Pfam ID:PF01165
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S22, mitochondrial
Gene (Uniprot):MRPS22
Chain IDs:R
Chain Length:360
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82650 Pfam ID:PF10245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S23, mitochondrial
Gene (Uniprot):MRPS23
Chain IDs:S
Chain Length:190
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3D9 Pfam ID:PF10484
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S25, mitochondrial
Gene (Uniprot):MRPS25
Chain IDs:T
Chain Length:173
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P82663 Pfam ID:PF05047
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S26, mitochondrial
Gene (Uniprot):MRPS26
Chain IDs:U
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYN8 Pfam ID:PF14943
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S27, mitochondrial
Gene (Uniprot):MRPS27
Chain IDs:V
Chain Length:414
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92552 Pfam ID:PF10037
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S28, mitochondrial
Gene (Uniprot):MRPS28
Chain IDs:W
Chain Length:187
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y2Q9 Pfam ID:PF10246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S29, mitochondrial
Gene (Uniprot):DAP3
Chain IDs:X
Chain Length:398
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P51398 Pfam ID:PF10236
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S31, mitochondrial
Gene (Uniprot):MRPS31
Chain IDs:Y
Chain Length:395
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92665 Pfam ID:PF15433
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S33, mitochondrial
Gene (Uniprot):MRPS33
Chain IDs:Z
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y291 Pfam ID:PF08293
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Putative ribosome-binding factor A, mitochondrial
Gene (Uniprot):RBFA
Chain IDs:EA (auth: a)
Chain Length:343
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N0V3 Pfam ID:PF02033
Protein Blast
Polymer Type:polypeptide(L)
Molecule:12S rRNA N4-methylcytidine (m4C) methyltransferase
Gene (Uniprot):METTL15
Chain IDs:FA (auth: b)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:A6NJ78 Pfam ID:PF01795
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
AYA Q ALA modified residue
Ligand Molecules
ATP
FES
GDP
K
MG
NAD
SAH
ZN
Primary Citation
Mechanism of mitoribosomal small subunit biogenesis and preinitiation.
Nature 606 603 608 (2022)
PMID: 35676484 DOI: 10.1038/s41586-022-04795-x

Abstact

Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. 1) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex2 that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.

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Disease

Primary Citation of related structures
7PNY