7PNY image
Deposition Date 2021-09-08
Release Date 2022-06-15
Last Version Date 2025-12-10
Entry Detail
PDB ID:
7PNY
Keywords:
Title:
Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation b
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
3.06 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S34, mi
Gene (Uniprot):MRPS34
Chain IDs:AA (auth: 0)
Chain Length:218
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S35, mi
Gene (Uniprot):MRPS35
Chain IDs:BA (auth: 1)
Chain Length:323
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Aurora kinase A-interacting p
Gene (Uniprot):AURKAIP1
Chain IDs:CA (auth: 3)
Chain Length:199
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pentatricopeptide repeat doma
Gene (Uniprot):PTCD3
Chain IDs:DA (auth: 4)
Chain Length:689
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:12S mitochondrial rRNA
Chain IDs:A
Chain Length:343
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S2, mit
Gene (Uniprot):MRPS2
Chain IDs:B
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S24, mi
Gene (Uniprot):MRPS24
Chain IDs:C
Chain Length:167
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S5, mit
Gene (Uniprot):MRPS5
Chain IDs:D
Chain Length:430
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S6, mit
Gene (Uniprot):MRPS6
Chain IDs:E
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S7, mit
Gene (Uniprot):MRPS7
Chain IDs:F
Chain Length:242
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S9, mit
Gene (Uniprot):MRPS9
Chain IDs:G
Chain Length:396
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S10, mi
Gene (Uniprot):MRPS10
Chain IDs:H
Chain Length:201
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S11, mi
Gene (Uniprot):MRPS11
Chain IDs:I
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S12, mi
Gene (Uniprot):MRPS12
Chain IDs:J
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S14, mi
Gene (Uniprot):MRPS14
Chain IDs:K
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S15, mi
Gene (Uniprot):MRPS15
Chain IDs:L
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S16, mi
Gene (Uniprot):MRPS16
Chain IDs:M
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S17, mi
Gene (Uniprot):MRPS17
Chain IDs:N
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S18b, m
Gene (Uniprot):MRPS18B
Chain IDs:O
Chain Length:258
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S18c, m
Gene (Uniprot):MRPS18C
Chain IDs:P
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S21, mi
Gene (Uniprot):MRPS21
Chain IDs:Q
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S22, mi
Gene (Uniprot):MRPS22
Chain IDs:R
Chain Length:360
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S23, mi
Gene (Uniprot):MRPS23
Chain IDs:S
Chain Length:190
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S25, mi
Gene (Uniprot):MRPS25
Chain IDs:T
Chain Length:173
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S26, mi
Gene (Uniprot):MRPS26
Chain IDs:U
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S27, mi
Gene (Uniprot):MRPS27
Chain IDs:V
Chain Length:414
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S28, mi
Gene (Uniprot):MRPS28
Chain IDs:W
Chain Length:187
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S29, mi
Gene (Uniprot):DAP3
Chain IDs:X
Chain Length:398
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S31, mi
Gene (Uniprot):MRPS31
Chain IDs:Y
Chain Length:395
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:28S ribosomal protein S33, mi
Gene (Uniprot):MRPS33
Chain IDs:Z
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Putative ribosome-binding fac
Gene (Uniprot):RBFA
Chain IDs:EA (auth: a)
Chain Length:343
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:12S rRNA N4-methylcytidine (m
Gene (Uniprot):METTL15
Chain IDs:FA (auth: b)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
AYA Q ALA modified residue
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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Primary Citation of related structures
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