7O9M image
Deposition Date 2021-04-16
Release Date 2021-06-30
Last Version Date 2025-04-09
Entry Detail
PDB ID:
7O9M
Keywords:
RIBOSOME
Title:
Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU module
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7O9M validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L32, mitochondrial
Gene (Uniprot):MRPL32
Chain IDs:AA (auth: 0)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYC8 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L33, mitochondrial
Gene (Uniprot):MRPL33
Chain IDs:BA (auth: 1)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75394 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L34, mitochondrial
Gene (Uniprot):MRPL34
Chain IDs:CA (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BQ48 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L35, mitochondrial
Gene (Uniprot):MRPL35
Chain IDs:DA (auth: 3)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NZE8 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L36, mitochondrial
Gene (Uniprot):MRPL36
Chain IDs:EA (auth: 4)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P0J6 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L37, mitochondrial
Gene (Uniprot):MRPL37
Chain IDs:FA (auth: 5)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BZE1 Pfam ID:PF07147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L38, mitochondrial
Gene (Uniprot):MRPL38
Chain IDs:GA (auth: 6)
Chain Length:380
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96DV4 Pfam ID:PF01161
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L39, mitochondrial
Gene (Uniprot):MRPL39
Chain IDs:HA (auth: 7)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NYK5
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L40, mitochondrial
Gene (Uniprot):MRPL40
Chain IDs:IA (auth: 8)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NQ50 Pfam ID:PF09812
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L41, mitochondrial
Gene (Uniprot):MRPL41
Chain IDs:JA (auth: 9)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8IXM3 Pfam ID:PF09809
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:5-methylcytosine rRNA methyltransferase NSUN4
Gene (Uniprot):NSUN4
Chain IDs:CB (auth: A1)
Chain Length:384
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96CB9 Pfam ID:PF01189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription termination factor 4, mitochondrial
Gene (Uniprot):MTERF4
Chain IDs:DB (auth: A2)
Chain Length:381
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z6M4 Pfam ID:PF02536
Polymer Type:polyribonucleotide
Molecule:MT-TRNAVAL
Chain IDs:B
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosome-associated GTPase 1
Gene (Uniprot):MTG1
Chain IDs:C
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BT17 Pfam ID:PF01926
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L2, mitochondrial
Gene (Uniprot):MRPL2
Chain IDs:D
Chain Length:302
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5T653 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L3, mitochondrial
Gene (Uniprot):MRPL3
Chain IDs:E
Chain Length:279
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P09001 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L4, mitochondrial
Gene (Uniprot):MRPL4
Chain IDs:F
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD3 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L9, mitochondrial
Gene (Uniprot):MRPL9
Chain IDs:G (auth: H)
Chain Length:267
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD2 Pfam ID:PF01281, PF22078
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L10, mitochondrial
Gene (Uniprot):MRPL10
Chain IDs:H (auth: I)
Chain Length:261
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z7H8 Pfam ID:PF00466
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L11, mitochondrial
Gene (Uniprot):MRPL11
Chain IDs:I (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3B7 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L13, mitochondrial
Gene (Uniprot):MRPL13
Chain IDs:J (auth: K)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD1 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L14, mitochondrial
Gene (Uniprot):MRPL14
Chain IDs:K (auth: L)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P1L8 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L15, mitochondrial
Gene (Uniprot):MRPL15
Chain IDs:L (auth: M)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P015 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L16, mitochondrial
Gene (Uniprot):MRPL16
Chain IDs:M (auth: N)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NX20 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L17, mitochondrial
Gene (Uniprot):MRPL17
Chain IDs:N (auth: O)
Chain Length:175
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NRX2 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L18, isoform CRA_b
Gene (Uniprot):MRPL18
Chain IDs:O (auth: P)
Chain Length:179
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:A8K9D2 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L19, mitochondrial
Gene (Uniprot):MRPL19
Chain IDs:P (auth: Q)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P49406 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L20, mitochondrial
Gene (Uniprot):MRPL20
Chain IDs:Q (auth: R)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYC9 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L21, mitochondrial
Gene (Uniprot):MRPL21
Chain IDs:R (auth: S)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z2W9 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L22, mitochondrial
Gene (Uniprot):MRPL22
Chain IDs:S (auth: T)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:E7ESL0 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L23, mitochondrial
Gene (Uniprot):MRPL23
Chain IDs:T (auth: U)
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q16540 Pfam ID:PF00276
Polymer Type:polypeptide(L)
Molecule:Unknown residues
Chain IDs:NB (auth: UNK)
Chain Length:26
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L24, mitochondrial
Gene (Uniprot):MRPL24
Chain IDs:U (auth: V)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96A35 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L27, mitochondrial
Gene (Uniprot):MRPL27
Chain IDs:V (auth: W)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P0M9 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L28, mitochondrial
Gene (Uniprot):MRPL28
Chain IDs:W (auth: X)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13084 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L47, mitochondrial
Gene (Uniprot):MRPL47
Chain IDs:X (auth: Y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9HD33 Pfam ID:PF06984
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L30, mitochondrial
Gene (Uniprot):MRPL30
Chain IDs:Y (auth: Z)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TCC3 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L42, mitochondrial
Gene (Uniprot):MRPL42
Chain IDs:Z (auth: a)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y6G3 Pfam ID:PF10210
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L43, mitochondrial
Gene (Uniprot):MRPL43
Chain IDs:KA (auth: b)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N983 Pfam ID:PF05047
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L44, mitochondrial
Gene (Uniprot):MRPL44
Chain IDs:LA (auth: c)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H9J2 Pfam ID:PF22935, PF22892
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L45, mitochondrial
Gene (Uniprot):MRPL45
Chain IDs:MA (auth: d)
Chain Length:302
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BRJ2 Pfam ID:PF04280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L46, mitochondrial
Gene (Uniprot):MRPL46
Chain IDs:NA (auth: e)
Chain Length:279
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H2W6 Pfam ID:PF11788
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L48, mitochondrial
Gene (Uniprot):MRPL48
Chain IDs:OA (auth: f)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96GC5 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L49, mitochondrial
Gene (Uniprot):MRPL49
Chain IDs:PA (auth: g)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13405 Pfam ID:PF05046
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L50, mitochondrial
Gene (Uniprot):MRPL50
Chain IDs:QA (auth: h)
Chain Length:267
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N5N7 Pfam ID:PF10501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L51, mitochondrial
Gene (Uniprot):MRPL51
Chain IDs:RA (auth: i)
Chain Length:261
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q4U2R6 Pfam ID:PF10244
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L52, mitochondrial
Gene (Uniprot):MRPL52
Chain IDs:SA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q86TS9 Pfam ID:PF18699
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L53, mitochondrial
Gene (Uniprot):MRPL53
Chain IDs:TA (auth: k)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EL3 Pfam ID:PF10780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L54, mitochondrial
Gene (Uniprot):MRPL54
Chain IDs:UA (auth: l)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P161 Pfam ID:PF08561
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L55, mitochondrial
Gene (Uniprot):MRPL55
Chain IDs:VA (auth: m)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z7F7 Pfam ID:PF09776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA methyltransferase 2, mitochondrial
Gene (Uniprot):MRM2
Chain IDs:BB (auth: n)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UI43 Pfam ID:PF01728 EC:2.1.1.166
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein 63, mitochondrial
Gene (Uniprot):MRPL57
Chain IDs:WA (auth: o)
Chain Length:175
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BQC6 Pfam ID:PF14978
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Gene (Uniprot):MRPL58
Chain IDs:XA (auth: p)
Chain Length:179
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q14197 Pfam ID:PF00472 EC:3.1.1.29
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Growth arrest and DNA damage-inducible proteins-interacting protein 1
Gene (Uniprot):GADD45GIP1
Chain IDs:YA (auth: q)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TAE8 Pfam ID:PF10147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S18a, mitochondrial
Gene (Uniprot):MRPS18A
Chain IDs:ZA (auth: r)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVS2 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S30, mitochondrial
Gene (Uniprot):MRPS30
Chain IDs:AB (auth: s)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NP92 Pfam ID:PF07147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L12, mitochondrial
Gene (Uniprot):MRPL12
Chain IDs:GB (auth: t1), HB (auth: t2), IB (auth: t3), JB (auth: t4), KB (auth: t6), LB (auth: t5)
Chain Length:198
Number of Molecules:6
Biological Source:Homo sapiens
UniProt ID:P52815 Pfam ID:PF16320, PF00542
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial assembly of ribosomal large subunit protein 1
Gene (Uniprot):MALSU1
Chain IDs:FB (auth: u)
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EH3 Pfam ID:PF02410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:MIEF1 upstream open reading frame protein
Gene (Uniprot):MIEF1
Chain IDs:EB (auth: v)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:L0R8F8 Pfam ID:PF05347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitochondrial
Gene (Uniprot):NDUFAB1
Chain IDs:MB (auth: w)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O14561 Pfam ID:PF00550
Ligand Molecules
GDP
MG
PNS
SAM
ZN
Primary Citation
Structural basis for late maturation steps of the human mitoribosomal large subunit.
Nat Commun 12 3673 3673 (2021)
PMID: 34135318 DOI: 10.1038/s41467-021-23617-8

Abstact

Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood. Here, we determine the cryo-EM structures of mitoribosomes isolated from human cell lines with either depleted or overexpressed mitoribosome assembly factor GTPBP5, allowing us to capture consecutive steps during mitoribosomal large subunit (mt-LSU) biogenesis. Our structures provide essential insights into the last steps of 16S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, which require the coordinated action of nine assembly factors. We show that mammalian-specific MTERF4 contributes to the folding of 16S rRNA, allowing 16 S rRNA methylation by MRM2, while GTPBP5 and NSUN4 promote fine-tuning rRNA rearrangements leading to PTC formation. Moreover, our data reveal an unexpected involvement of the elongation factor mtEF-Tu in mt-LSU assembly, where mtEF-Tu interacts with GTPBP5, similar to its interaction with tRNA during translational elongation.

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Protein

Chemical

Disease

Primary Citation of related structures
7O9M