8PK0 image
Deposition Date 2023-06-23
Release Date 2023-12-13
Last Version Date 2025-10-01
Entry Detail
PDB ID:
8PK0
Keywords:
RIBOSOME
Title:
human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.03 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8PK0 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L32, mitochondrial
Gene (Uniprot):MRPL32
Chain IDs:A (auth: 0)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYC8 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L33, mitochondrial
Gene (Uniprot):MRPL33
Chain IDs:D (auth: 1)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75394 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L34, mitochondrial
Gene (Uniprot):MRPL34
Chain IDs:G (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BQ48 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L35, mitochondrial
Gene (Uniprot):MRPL35
Chain IDs:J (auth: 3)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NZE8 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L37, mitochondrial
Gene (Uniprot):MRPL37
Chain IDs:M (auth: 5)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BZE1 Pfam ID:PF07147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L38, mitochondrial
Gene (Uniprot):MRPL38
Chain IDs:P (auth: 6)
Chain Length:380
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96DV4 Pfam ID:PF01161
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L39, mitochondrial
Gene (Uniprot):MRPL39
Chain IDs:S (auth: 7)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NYK5
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L40, mitochondrial
Gene (Uniprot):MRPL40
Chain IDs:U (auth: 8)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NQ50 Pfam ID:PF09812
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L41, mitochondrial
Gene (Uniprot):MRPL41
Chain IDs:W (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 + pre-H68-71 segment
Chain IDs:Y (auth: A)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:CP tRNA-Val
Chain IDs:AA (auth: B)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L2, mitochondrial
Gene (Uniprot):MRPL2
Chain IDs:CA (auth: D)
Chain Length:305
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5T653 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L3, mitochondrial
Gene (Uniprot):MRPL3
Chain IDs:EA (auth: E)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P09001 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L4, mitochondrial
Gene (Uniprot):MRPL4
Chain IDs:GA (auth: F)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD3 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L9, mitochondrial
Gene (Uniprot):MRPL9
Chain IDs:IA (auth: H)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD2 Pfam ID:PF01281, PF22078
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L10, mitochondrial
Gene (Uniprot):MRPL10
Chain IDs:KA (auth: I)
Chain Length:261
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z7H8 Pfam ID:PF00466
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L11, mitochondrial
Gene (Uniprot):MRPL11
Chain IDs:MA (auth: J)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3B7 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L13, mitochondrial
Gene (Uniprot):MRPL13
Chain IDs:OA (auth: K)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD1 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L14, mitochondrial
Gene (Uniprot):MRPL14
Chain IDs:QA (auth: L)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P1L8 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L15, mitochondrial
Gene (Uniprot):MRPL15
Chain IDs:SA (auth: M)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P015 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L16, mitochondrial
Gene (Uniprot):MRPL16
Chain IDs:UA (auth: N)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NX20 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L17, mitochondrial
Gene (Uniprot):MRPL17
Chain IDs:WA (auth: O)
Chain Length:175
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NRX2 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L18, mitochondrial
Gene (Uniprot):MRPL18
Chain IDs:YA (auth: P)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H0U6 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L19, mitochondrial
Gene (Uniprot):MRPL19
Chain IDs:AB (auth: Q)
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P49406 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L20, mitochondrial
Gene (Uniprot):MRPL20
Chain IDs:CB (auth: R)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYC9 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L21, mitochondrial
Gene (Uniprot):MRPL21
Chain IDs:EB (auth: S)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z2W9 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L22, mitochondrial
Gene (Uniprot):MRPL22
Chain IDs:B (auth: T)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NWU5 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L23, mitochondrial
Gene (Uniprot):MRPL23
Chain IDs:E (auth: U)
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q16540 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L24, mitochondrial
Gene (Uniprot):MRPL24
Chain IDs:H (auth: V)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96A35 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L27, mitochondrial
Gene (Uniprot):MRPL27
Chain IDs:K (auth: W)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P0M9 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L28, mitochondrial
Gene (Uniprot):MRPL28
Chain IDs:N (auth: X)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13084 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L47, mitochondrial
Gene (Uniprot):MRPL47
Chain IDs:Q (auth: Y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9HD33 Pfam ID:PF06984
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L30, mitochondrial
Gene (Uniprot):MRPL30
Chain IDs:T (auth: Z)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TCC3 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L42, mitochondrial
Gene (Uniprot):MRPL42
Chain IDs:V (auth: a)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y6G3 Pfam ID:PF10210
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL43
Gene (Uniprot):MRPL43
Chain IDs:X (auth: b)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N983 Pfam ID:PF05047
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L44, mitochondrial
Gene (Uniprot):MRPL44
Chain IDs:Z (auth: c)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H9J2 Pfam ID:PF22935, PF22892
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L45, mitochondrial
Gene (Uniprot):MRPL45
Chain IDs:BA (auth: d)
Chain Length:305
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BRJ2 Pfam ID:PF04280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L46, mitochondrial
Gene (Uniprot):MRPL46
Chain IDs:DA (auth: e)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H2W6 Pfam ID:PF11788
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L48, mitochondrial
Gene (Uniprot):MRPL48
Chain IDs:FA (auth: f)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96GC5 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L49, mitochondrial
Gene (Uniprot):MRPL49
Chain IDs:HA (auth: g)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13405 Pfam ID:PF05046
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L50, mitochondrial
Gene (Uniprot):MRPL50
Chain IDs:JA (auth: h)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N5N7 Pfam ID:PF10501
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L51, mitochondrial
Gene (Uniprot):MRPL51
Chain IDs:LA (auth: i)
Chain Length:261
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q4U2R6 Pfam ID:PF10244
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L52, mitochondrial
Gene (Uniprot):MRPL52
Chain IDs:NA (auth: j)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q86TS9 Pfam ID:PF18699
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L53, mitochondrial
Gene (Uniprot):MRPL53
Chain IDs:PA (auth: k)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EL3 Pfam ID:PF10780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L54, mitochondrial
Gene (Uniprot):MRPL54
Chain IDs:RA (auth: l)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P161 Pfam ID:PF08561
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L55, mitochondrial
Gene (Uniprot):MRPL55
Chain IDs:TA (auth: m)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z7F7 Pfam ID:PF09776
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein 63, mitochondrial
Gene (Uniprot):MRPL57
Chain IDs:VA (auth: o)
Chain Length:175
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BQC6 Pfam ID:PF14978
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Gene (Uniprot):MRPL58
Chain IDs:XA (auth: p)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q14197 Pfam ID:PF00472 EC:3.1.1.29
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Growth arrest and DNA damage-inducible proteins-interacting protein 1
Gene (Uniprot):GADD45GIP1
Chain IDs:ZA (auth: q)
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TAE8 Pfam ID:PF10147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S18a, mitochondrial
Gene (Uniprot):MRPS18A
Chain IDs:BB (auth: r)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVS2 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S30, mitochondrial
Gene (Uniprot):MRPS30
Chain IDs:DB (auth: s)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NP92 Pfam ID:PF07147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GTP-binding protein 10
Gene (Uniprot):GTPBP10
Chain IDs:FB (auth: t)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:A4D1E9 Pfam ID:PF01018, PF01926
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial assembly of ribosomal large subunit protein 1
Gene (Uniprot):MALSU1
Chain IDs:C (auth: u)
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EH3 Pfam ID:PF02410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:MIEF1 upstream open reading frame protein
Gene (Uniprot):MIEF1
Chain IDs:F (auth: v)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:L0R8F8 Pfam ID:PF05347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitochondrial
Gene (Uniprot):NDUFAB1
Chain IDs:I (auth: w)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O14561 Pfam ID:PF00550
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:5-methylcytosine rRNA methyltransferase NSUN4
Gene (Uniprot):NSUN4
Chain IDs:L (auth: x)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96CB9 Pfam ID:PF01189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription termination factor 4, mitochondrial
Gene (Uniprot):MTERF4
Chain IDs:O (auth: y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z6M4 Pfam ID:PF02536
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosome-associated GTPase 1
Gene (Uniprot):MTG1
Chain IDs:R (auth: z)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BT17 Pfam ID:PF01926
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
AYA E ALA modified residue
SAC OA SER modified residue
Ligand Molecules
GNP
K
MG
PM8
SAM
ZN
Primary Citation
Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome.
Nat Commun 14 7991 7991 (2023)
PMID: 38042949 DOI: 10.1038/s41467-023-43599-z

Abstact

Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ribosomal proteins. Assembly is coordinated in the mitochondrial matrix by biogenesis factors that transiently associate with the maturing particle. Here, we present a structural snapshot of a large mitoribosomal subunit assembly intermediate containing 7 biogenesis factors including the GTPases GTPBP7 and GTPBP10. Our structure illustrates how GTPBP10 aids the folding of the ribosomal RNA during the biogenesis process, how this process is related to bacterial ribosome biogenesis, and why mitochondria require two biogenesis factors in contrast to only one in bacteria.

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Protein

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Disease

Primary Citation of related structures
8PK0
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