ISDA

Deposition Date 2021-04-30

Release Date 2021-06-23

Last Version Date 2023-11-15

Entry Detail

PDB ID:

7ODS

Keywords:

RIBOSOME

Title:

State B of the human mitoribosomal large subunit assembly intermediate

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.10 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L32, mitochondrial
Gene (Uniprot):MRPL32
Chain IDs:G (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:H (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:I (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:J (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:K (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:L (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:M (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:N (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:O (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:P (auth: 9)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8IXM3 Pfam ID:PF09809

Polymer Type:polyribonucleotide
Molecule:16S mitochondrial rRNA, DNA (30-MER),16S mitochondrial rRNA
Chain IDs:Q (auth: A)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:mitochondrial tRNAVal
Chain IDs:R (auth: B)
Chain Length:72
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L2, mitochondrial
Gene (Uniprot):MRPL2
Chain IDs:S (auth: D)
Chain Length:306
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:T (auth: E)
Chain Length:348
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:U (auth: F)
Chain Length:311
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:V (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:W (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)
Molecule:39S ribosomal protein L11, mitochondrial
Gene (Uniprot):MRPL11
Chain IDs:X (auth: J)
Chain Length:192
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:Y (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:Z (auth: L)
Chain Length:145
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:AA (auth: M)
Chain Length:296
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:BA (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:CA (auth: O)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NRX2 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L18, mitochondrial
Gene (Uniprot):MRPL18
Chain IDs:DA (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)
Molecule:39S ribosomal protein L19, mitochondrial
Gene (Uniprot):MRPL19
Chain IDs:EA (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)
Molecule:39S ribosomal protein L20, mitochondrial
Gene (Uniprot):MRPL20
Chain IDs:FA (auth: R)
Chain Length:149
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:GA (auth: S)
Chain Length:205
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:HA (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)
Molecule:39S ribosomal protein L23, mitochondrial
Gene (Uniprot):MRPL23
Chain IDs:IA (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)
Molecule:39S ribosomal protein L24, mitochondrial
Gene (Uniprot):MRPL24
Chain IDs:JA (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:KA (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:LA (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:MA (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:NA (auth: Z)
Chain Length:246
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:OA (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:PA (auth: b)
Chain Length:72
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:QA (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:RA (auth: d)
Chain Length:306
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:SA (auth: e)
Chain Length:348
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:TA (auth: f)
Chain Length:311
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:UA (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:VA (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:WA (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)
Molecule:39S ribosomal protein L52, mitochondrial
Gene (Uniprot):MRPL52
Chain IDs:XA (auth: j)
Chain Length:192
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:YA (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:ZA (auth: l)
Chain Length:145
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:AB (auth: m)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z7F7 Pfam ID:PF09776

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein 63, mitochondrial
Gene (Uniprot):MRPL57
Chain IDs:BB (auth: o)
Chain Length:102
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:CB (auth: p)
Chain Length:180
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:DB (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)
Molecule:39S ribosomal protein S18a, mitochondrial
Gene (Uniprot):MRPS18A
Chain IDs:EB (auth: r)
Chain Length:149
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:FB (auth: s)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NP92 Pfam ID:PF07147

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial assembly of ribosomal large subunit protein 1
Gene (Uniprot):MALSU1
Chain IDs:A (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)
Molecule:MIEF1 upstream open reading frame protein
Gene (Uniprot):MIEF1
Chain IDs:B (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:C (auth: w)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O14561 Pfam ID:PF00550

Protein Blast

Polymer Type:polypeptide(L)
Molecule:5-methylcytosine rRNA methyltransferase NSUN4
Gene (Uniprot):NSUN4
Chain IDs:D (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)
Molecule:Transcription termination factor 4, mitochondrial
Gene (Uniprot):MTERF4
Chain IDs:E (auth: y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z6M4 Pfam ID:PF02536

Protein Blast

Polymer Type:polypeptide(L)
Molecule:rRNA methyltransferase 2, mitochondrial
Gene (Uniprot):MRM2
Chain IDs:F (auth: z)
Chain Length:246
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UI43 Pfam ID:PF01728 EC:2.1.1.166

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
AYA	IA	ALA	modified residue
SAC	Y	SER	modified residue
THC	PA	THR	modified residue

Ligand Molecules

FES

PM8

SAM

Primary Citation

Stepwise maturation of the peptidyl transferase region of human mitoribosomes.

Lenarcic, T, Jaskolowski, M, Leibundgut, M, Scaiola, A, Schonhut, T, Saurer, M, Lee, R.G, Rackham, O, Filipovska, A, Ban, N.Show

Nat Commun 12 3671 3671 (2021)

PMID: 34135320 DOI: 10.1038/s41467-021-23811-8

Abstact

Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.

Legend

Protein

Chemical

Disease

Primary Citation of related structures