7OIC image
Deposition Date 2021-05-11
Release Date 2021-09-15
Last Version Date 2021-10-13
Entry Detail
PDB ID:
7OIC
Keywords:
Title:
Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L32, mitochondrial
Gene (Uniprot):MRPL32
Chain IDs:Y (auth: 0)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L33, mitochondrial
Gene (Uniprot):MRPL33
Chain IDs:Z (auth: 1)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L34, mitochondrial
Gene (Uniprot):MRPL34
Chain IDs:AA (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L35, mitochondrial
Gene (Uniprot):MRPL35
Chain IDs:BA (auth: 3)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L36, mitochondrial
Gene (Uniprot):MRPL36
Chain IDs:CA (auth: 4)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L37, mitochondrial
Gene (Uniprot):MRPL37
Chain IDs:DA (auth: 5)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L38, mitochondrial
Gene (Uniprot):MRPL38
Chain IDs:EA (auth: 6)
Chain Length:380
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L39, mitochondrial
Gene (Uniprot):MRPL39
Chain IDs:FA (auth: 7)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L40, mitochondrial
Gene (Uniprot):MRPL40
Chain IDs:GA (auth: 8)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L41, mitochondrial
Gene (Uniprot):MRPL41
Chain IDs:HA (auth: 9)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A
Chain Length:1559
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:mitochondrial Val tRNA
Chain IDs:B
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L2, mitochondrial
Gene (Uniprot):MRPL2
Chain IDs:C (auth: D)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L3, mitochondrial
Gene (Uniprot):MRPL3
Chain IDs:D (auth: E)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L4, mitochondrial
Gene (Uniprot):MRPL4
Chain IDs:E (auth: F)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L9, mitochondrial
Gene (Uniprot):MRPL9
Chain IDs:F (auth: H)
Chain Length:267
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L10, mitochondrial
Gene (Uniprot):MRPL10
Chain IDs:G (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L11, mitochondrial
Gene (Uniprot):MRPL11
Chain IDs:H (auth: J)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L13, mitochondrial
Gene (Uniprot):MRPL13
Chain IDs:I (auth: K)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L14, mitochondrial
Gene (Uniprot):MRPL14
Chain IDs:J (auth: L)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L15, mitochondrial
Gene (Uniprot):MRPL15
Chain IDs:K (auth: M)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L16, mitochondrial
Gene (Uniprot):MRPL16
Chain IDs:L (auth: N)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L17, mitochondrial
Gene (Uniprot):MRPL17
Chain IDs:M (auth: O)
Chain Length:175
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L18, mitochondrial
Gene (Uniprot):MRPL18
Chain IDs:N (auth: P)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L19, mitochondrial
Gene (Uniprot):MRPL19
Chain IDs:O (auth: Q)
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L20, mitochondrial
Gene (Uniprot):MRPL20
Chain IDs:P (auth: R)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L21, mitochondrial
Gene (Uniprot):MRPL21
Chain IDs:Q (auth: S)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L22, mitochondrial
Gene (Uniprot):MRPL22
Chain IDs:R (auth: T)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L23, mitochondrial
Gene (Uniprot):MRPL23
Chain IDs:S (auth: U)
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L24, mitochondrial
Gene (Uniprot):MRPL24
Chain IDs:T (auth: V)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L27, mitochondrial
Gene (Uniprot):MRPL27
Chain IDs:U (auth: W)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L28, mitochondrial
Gene (Uniprot):MRPL28
Chain IDs:V (auth: X)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L47, mitochondrial
Gene (Uniprot):MRPL47
Chain IDs:W (auth: Y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L30, mitochondrial
Gene (Uniprot):MRPL30
Chain IDs:X (auth: Z)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L42, mitochondrial
Gene (Uniprot):MRPL42
Chain IDs:IA (auth: a)
Chain Length:1559
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L43, mitochondrial
Gene (Uniprot):MRPL43
Chain IDs:JA (auth: b)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L44, mitochondrial
Gene (Uniprot):MRPL44
Chain IDs:KA (auth: c)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L45, mitochondrial
Gene (Uniprot):MRPL45
Chain IDs:LA (auth: d)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L46, mitochondrial
Gene (Uniprot):MRPL46
Chain IDs:MA (auth: e)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L48, mitochondrial
Gene (Uniprot):MRPL48
Chain IDs:NA (auth: f)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L49, mitochondrial
Gene (Uniprot):MRPL49
Chain IDs:OA (auth: g)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L50, mitochondrial
Gene (Uniprot):MRPL50
Chain IDs:PA (auth: h)
Chain Length:267
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L51, mitochondrial
Gene (Uniprot):MRPL51
Chain IDs:QA (auth: i)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L52, mitochondrial
Gene (Uniprot):MRPL52
Chain IDs:RA (auth: j)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L53, mitochondrial
Gene (Uniprot):MRPL53
Chain IDs:SA (auth: k)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L54, mitochondrial
Gene (Uniprot):MRPL54
Chain IDs:TA (auth: l)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L55, mitochondrial
Gene (Uniprot):MRPL55
Chain IDs:UA (auth: m)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
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
Polymer Type:polypeptide(L)
Molecule:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Gene (Uniprot):MRPL58
Chain IDs:WA (auth: p)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Growth arrest and DNA damage-inducible proteins-interacting protein 1
Gene (Uniprot):GADD45GIP1
Chain IDs:XA (auth: q)
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S18a, mitochondrial
Gene (Uniprot):MRPS18A
Chain IDs:YA (auth: r)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S30, mitochondrial
Gene (Uniprot):MRPS30
Chain IDs:ZA (auth: s)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Mitochondrial assembly of ribosomal large subunit protein 1
Gene (Uniprot):MALSU1
Chain IDs:AB (auth: u)
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:MIEF1 upstream open reading frame protein
Gene (Uniprot):MIEF1
Chain IDs:BB (auth: v)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitochondrial
Gene (Uniprot):NDUFAB1
Chain IDs:CB (auth: w)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:5-methylcytosine rRNA methyltransferase NSUN4
Gene (Uniprot):NSUN4
Chain IDs:DB (auth: x)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Transcription termination factor 4, mitochondrial
Gene (Uniprot):MTERF4
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.

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Primary Citation of related structures