ISDA

Entry Detail

PDB ID:

8QSJ

EMDB ID:

EMD-17720

Keywords:

RIBOSOME

Title:

Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7

Biological Source:

Source Organism:

Homo sapiens

PDB Version:

Deposition Date:

2023-10-10

Release Date:

2023-12-13

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.00 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L32, mitochondrial
Chain IDs:A (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)
Description:39S ribosomal protein L33, mitochondrial
Chain IDs:B (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)
Description:39S ribosomal protein L34, mitochondrial
Chain IDs:C (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)
Description:39S ribosomal protein L35, mitochondrial
Chain IDs:D (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)
Description:39S ribosomal protein L36, mitochondrial
Chain IDs:E (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)
Description:39S ribosomal protein L37, mitochondrial
Chain IDs:F (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)
Description:39S ribosomal protein L38, mitochondrial
Chain IDs:G (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)
Description:39S ribosomal protein L39, mitochondrial
Chain IDs:H (auth: 7)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NYK5

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L40, mitochondrial
Chain IDs:I (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)
Description:39S ribosomal protein L41, mitochondrial
Chain IDs:J (auth: 9)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8IXM3 Pfam ID:PF09809

Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:K (auth: A)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Description:tRNA-Val
Chain IDs:L (auth: B)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L2, mitochondrial
Chain IDs:M (auth: D)
Chain Length:305
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q5T653 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L3, mitochondrial
Chain IDs:N (auth: E)
Chain Length:279
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P09001 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L4, mitochondrial
Chain IDs:O (auth: F)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYD3 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L9, mitochondrial
Chain IDs:P (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)
Description:39S ribosomal protein L10, mitochondrial
Chain IDs:Q (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z7H8 Pfam ID:PF00466

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L11, mitochondrial
Chain IDs:R (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)
Description:39S ribosomal protein L13, mitochondrial
Chain IDs:S (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)
Description:39S ribosomal protein L14, mitochondrial
Chain IDs:T (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)
Description:39S ribosomal protein L15, mitochondrial
Chain IDs:U (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)
Description:39S ribosomal protein L16, mitochondrial
Chain IDs:V (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)
Description:39S ribosomal protein L17, mitochondrial
Chain IDs:W (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)
Description:39S ribosomal protein L18, mitochondrial
Chain IDs:X (auth: P)
Chain Length:180
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H0U6 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L19, mitochondrial
Chain IDs:Y (auth: Q)
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P49406 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L20, mitochondrial
Chain IDs:Z (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)
Description:39S ribosomal protein L21, mitochondrial
Chain IDs:AA (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)
Description:39S ribosomal protein L22, mitochondrial
Chain IDs:BA (auth: T)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NWU5 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L23, mitochondrial
Chain IDs:CA (auth: U)
Chain Length:153
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q16540 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L24, mitochondrial
Chain IDs:DA (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)
Description:39S ribosomal protein L27, mitochondrial
Chain IDs:EA (auth: W)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9P0M9 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L28, mitochondrial
Chain IDs:FA (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)
Description:39S ribosomal protein L47, mitochondrial
Chain IDs:GA (auth: Y)
Chain Length:381
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9HD33 Pfam ID:PF06984

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L30, mitochondrial
Chain IDs:HA (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)
Description:39S ribosomal protein L42, mitochondrial
Chain IDs:IA (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)
Description:Large ribosomal subunit protein mL43
Chain IDs:JA (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)
Description:39S ribosomal protein L44, mitochondrial
Chain IDs:KA (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)
Description:39S ribosomal protein L45, mitochondrial
Chain IDs:LA (auth: d)
Chain Length:305
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BRJ2 Pfam ID:PF04280

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L46, mitochondrial
Chain IDs:MA (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)
Description:39S ribosomal protein L48, mitochondrial
Chain IDs:NA (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)
Description:39S ribosomal protein L49, mitochondrial
Chain IDs:OA (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)
Description:39S ribosomal protein L50, mitochondrial
Chain IDs:PA (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)
Description:39S ribosomal protein L51, mitochondrial
Chain IDs:QA (auth: i)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q4U2R6 Pfam ID:PF10244

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein L52, mitochondrial
Chain IDs:RA (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)
Description:39S ribosomal protein L53, mitochondrial
Chain IDs:SA (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)
Description:39S ribosomal protein L54, mitochondrial
Chain IDs:TA (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)
Description:39S ribosomal protein L55, mitochondrial
Chain IDs:UA (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)
Description:Ribosomal protein 63, mitochondrial
Chain IDs:VA (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)
Description:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Chain IDs:WA (auth: p)
Chain Length:180
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q14197 Pfam ID:PF00472

Protein Blast

Polymer Type:polypeptide(L)
Description:Growth arrest and DNA damage-inducible proteins-interacting protein 1
Chain IDs:XA (auth: q)
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8TAE8 Pfam ID:PF10147

Protein Blast

Polymer Type:polypeptide(L)
Description:39S ribosomal protein S18a, mitochondrial
Chain IDs:YA (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)
Description:39S ribosomal protein S30, mitochondrial
Chain IDs:ZA (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)
Description:Mitochondrial assembly of ribosomal large subunit protein 1
Chain IDs:AB (auth: u)
Chain Length:153
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96EH3 Pfam ID:PF02410

Protein Blast

Polymer Type:polypeptide(L)
Description:MIEF1 upstream open reading frame protein
Chain IDs:BB (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)
Description:Acyl carrier protein, mitochondrial
Chain IDs:CB (auth: w)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O14561 Pfam ID:PF00550

Protein Blast

Polymer Type:polypeptide(L)
Description:5-methylcytosine rRNA methyltransferase NSUN4
Chain IDs:DB (auth: x)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96CB9 Pfam ID:PF01189

Protein Blast

Polymer Type:polypeptide(L)
Description:Transcription termination factor 4, mitochondrial
Chain IDs:EB (auth: y)
Chain Length:381
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z6M4 Pfam ID:PF02536

Protein Blast

Polymer Type:polypeptide(L)
Description:Mitochondrial ribosome-associated GTPase 1
Chain IDs:FB (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	CA	ALA	modified residue
SAC	S	SER	modified residue

Ligand Molecules

FES

GNP

PM8

SAM

Primary Citation

Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome.

Nguyen, T.G, Ritter, C, Kummer, E.Show

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures