ISDA: 7ODS

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(s):

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L32, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L33, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L34, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L35, mi
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 L36, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L37, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L38, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L39, mi
Gene (Uniprot):MRPL39
Chain IDs:N (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, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L41, mi
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 (
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L2, mit
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L3, mit
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L4, mit
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L9, mit
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, PF25131

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L10, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L11, mi
Gene (Uniprot):MRPL11
Chain IDs:X (auth: J)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3B7 Pfam ID:PF00298, PF03946

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L13, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L14, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L15, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L16, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L17, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L18, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L19, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L20, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L21, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L22, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L23, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L24, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L27, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L28, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L47, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L30, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L42, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L43, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L44, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L45, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L46, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L48, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L49, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L50, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L51, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L52, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L53, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L54, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L55, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein 63, mitocho
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptidyl-tRNA hydrolase ICT1,
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Growth arrest and DNA damage-
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S18a, m
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S30, mi
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial assembly of rib
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:MIEF1 upstream open reading f
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitocho
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:5-methylcytosine rRNA methylt
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription termination fac
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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:rRNA methyltransferase 2, mit
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.

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Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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