7OIC image
Entry Detail
PDB ID:
7OIC
EMDB ID:
Keywords:
Title:
Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2021-05-11
Release Date:
2021-09-15
Method Details:
Experimental Method:
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L32, mitochondrial
Chain IDs:Y (auth: 0)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L33, mitochondrial
Chain IDs:Z (auth: 1)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L34, mitochondrial
Chain IDs:AA (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L35, mitochondrial
Chain IDs:BA (auth: 3)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L36, mitochondrial
Chain IDs:CA (auth: 4)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L37, mitochondrial
Chain IDs:DA (auth: 5)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L38, mitochondrial
Chain IDs:EA (auth: 6)
Chain Length:380
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L39, mitochondrial
Chain IDs:FA (auth: 7)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L40, mitochondrial
Chain IDs:GA (auth: 8)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L41, mitochondrial
Chain IDs:HA (auth: 9)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:A
Chain Length:1559
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:mitochondrial Val tRNA
Chain IDs:B
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L2, mitochondrial
Chain IDs:C (auth: D)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L3, mitochondrial
Chain IDs:D (auth: E)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L4, mitochondrial
Chain IDs:E (auth: F)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L9, mitochondrial
Chain IDs:F (auth: H)
Chain Length:267
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L10, mitochondrial
Chain IDs:G (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L11, mitochondrial
Chain IDs:H (auth: J)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L13, mitochondrial
Chain IDs:I (auth: K)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L14, mitochondrial
Chain IDs:J (auth: L)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L15, mitochondrial
Chain IDs:K (auth: M)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L16, mitochondrial
Chain IDs:L (auth: N)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L17, mitochondrial
Chain IDs:M (auth: O)
Chain Length:175
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L18, mitochondrial
Chain IDs:N (auth: P)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L19, mitochondrial
Chain IDs:O (auth: Q)
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L20, mitochondrial
Chain IDs:P (auth: R)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L21, mitochondrial
Chain IDs:Q (auth: S)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L22, mitochondrial
Chain IDs:R (auth: T)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L23, mitochondrial
Chain IDs:S (auth: U)
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L24, mitochondrial
Chain IDs:T (auth: V)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L27, mitochondrial
Chain IDs:U (auth: W)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L28, mitochondrial
Chain IDs:V (auth: X)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L47, mitochondrial
Chain IDs:W (auth: Y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L30, mitochondrial
Chain IDs:X (auth: Z)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L42, mitochondrial
Chain IDs:IA (auth: a)
Chain Length:1559
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L43, mitochondrial
Chain IDs:JA (auth: b)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
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
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L45, mitochondrial
Chain IDs:LA (auth: d)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L46, mitochondrial
Chain IDs:MA (auth: e)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
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
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
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
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
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L52, mitochondrial
Chain IDs:RA (auth: j)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
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
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
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
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
Polymer Type:polypeptide(L)
Description:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Chain IDs:WA (auth: p)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
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
Polymer Type:polypeptide(L)
Description:39S ribosomal protein S18a, mitochondrial
Chain IDs:YA (auth: r)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein S30, mitochondrial
Chain IDs:ZA (auth: s)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Mitochondrial assembly of ribosomal large subunit protein 1
Chain IDs:AB (auth: u)
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:MIEF1 upstream open reading frame protein
Chain IDs:BB (auth: v)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Acyl carrier protein, mitochondrial
Chain IDs:CB (auth: w)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
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
Polymer Type:polypeptide(L)
Description:Transcription termination factor 4, mitochondrial
Chain IDs:EB (auth: y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE DB MET modified residue
Primary Citation
A distinct assembly pathway of the human 39S late pre-mitoribosome.
Nat Commun 12 4544 4544 (2021)
PMID: 34315873 DOI: 10.1038/s41467-021-24818-x

Abstact

Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.

Legend

Protein

Chemical

Disease

Primary Citation of related structures