5OOM image
Deposition Date 2017-08-08
Release Date 2017-09-13
Last Version Date 2025-12-17
Entry Detail
PDB ID:
5OOM
Keywords:
RIBOSOME
Title:
Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.03 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5OOM validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L32, mi
Gene (Uniprot):MRPL32
Chain IDs:Y (auth: 0)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYC8 Pfam ID:PF01783
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L33, mi
Gene (Uniprot):MRPL33
Chain IDs:Z (auth: 1)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75394 Pfam ID:PF00471
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L34, mi
Gene (Uniprot):MRPL34
Chain IDs:AA (auth: 2)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BQ48 Pfam ID:PF00468
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L35, mi
Gene (Uniprot):MRPL35
Chain IDs:BA (auth: 3)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NZE8 Pfam ID:PF01632
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L37, mi
Gene (Uniprot):MRPL37
Chain IDs:CA (auth: 5)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BZE1 Pfam ID:PF07147
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L38, mi
Gene (Uniprot):MRPL38
Chain IDs:DA (auth: 6)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96DV4 Pfam ID:PF01161
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L39, mi
Gene (Uniprot):MRPL39
Chain IDs:EA (auth: 7)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NYK5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L40, mi
Gene (Uniprot):MRPL40
Chain IDs:FA (auth: 8)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NQ50 Pfam ID:PF09812
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L41, mi
Gene (Uniprot):MRPL41
Chain IDs:GA (auth: 9)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8IXM3 Pfam ID:PF09809
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:mitochondrial tRNAVal
Chain IDs:B
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L2, mit
Gene (Uniprot):MRPL2
Chain IDs:C (auth: D)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5T653 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L3, mit
Gene (Uniprot):MRPL3
Chain IDs:D (auth: E)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P09001 Pfam ID:PF00297
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L4, mit
Gene (Uniprot):MRPL4
Chain IDs:E (auth: F)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD3 Pfam ID:PF00573
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L9, mit
Gene (Uniprot):MRPL9
Chain IDs:F (auth: H)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD2 Pfam ID:PF01281, PF22078, PF25131
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L10, mi
Gene (Uniprot):MRPL10
Chain IDs:G (auth: I)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z7H8 Pfam ID:PF00466
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L11, mi
Gene (Uniprot):MRPL11
Chain IDs:H (auth: J)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3B7 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L13, mi
Gene (Uniprot):MRPL13
Chain IDs:I (auth: K)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD1 Pfam ID:PF00572
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L14, mi
Gene (Uniprot):MRPL14
Chain IDs:J (auth: L)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P1L8 Pfam ID:PF00238
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L15, mi
Gene (Uniprot):MRPL15
Chain IDs:K (auth: M)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P015 Pfam ID:PF00828
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L16, mi
Gene (Uniprot):MRPL16
Chain IDs:L (auth: N)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NX20 Pfam ID:PF00252
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L17, mi
Gene (Uniprot):MRPL17
Chain IDs:M (auth: O)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NRX2 Pfam ID:PF01196
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L18, mi
Gene (Uniprot):MRPL18
Chain IDs:N (auth: P)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H0U6 Pfam ID:PF00861
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L19, mi
Gene (Uniprot):MRPL19
Chain IDs:O (auth: Q)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P49406 Pfam ID:PF01245
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L20, mi
Gene (Uniprot):MRPL20
Chain IDs:P (auth: R)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYC9 Pfam ID:PF00453
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L21, mi
Gene (Uniprot):MRPL21
Chain IDs:Q (auth: S)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z2W9 Pfam ID:PF00829
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L22, mi
Gene (Uniprot):MRPL22
Chain IDs:R (auth: T)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NWU5 Pfam ID:PF00237
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L23, mi
Gene (Uniprot):MRPL23
Chain IDs:S (auth: U)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q16540 Pfam ID:PF00276
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L24, mi
Gene (Uniprot):MRPL24
Chain IDs:T (auth: V)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96A35 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L27, mi
Gene (Uniprot):MRPL27
Chain IDs:U (auth: W)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P0M9 Pfam ID:PF01016
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L28, mi
Gene (Uniprot):MRPL28
Chain IDs:V (auth: X)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13084 Pfam ID:PF00830
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L47, mi
Gene (Uniprot):MRPL47
Chain IDs:W (auth: Y)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9HD33 Pfam ID:PF06984
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L30, mi
Gene (Uniprot):MRPL30
Chain IDs:X (auth: Z)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TCC3 Pfam ID:PF00327
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L42, mi
Gene (Uniprot):MRPL42
Chain IDs:HA (auth: a)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y6G3 Pfam ID:PF10210
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L43, mi
Gene (Uniprot):MRPL43
Chain IDs:IA (auth: b)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N983 Pfam ID:PF05047
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L44, mi
Gene (Uniprot):MRPL44
Chain IDs:JA (auth: c)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H9J2 Pfam ID:PF22935, PF22892 EC:3.1.26.-
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L45, mi
Gene (Uniprot):MRPL45
Chain IDs:KA (auth: d)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BRJ2 Pfam ID:PF04280
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L46, mi
Gene (Uniprot):MRPL46
Chain IDs:LA (auth: e)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H2W6 Pfam ID:PF11788
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L48, mi
Gene (Uniprot):MRPL48
Chain IDs:MA (auth: f)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96GC5 Pfam ID:PF00338
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L49, mi
Gene (Uniprot):MRPL49
Chain IDs:NA (auth: g)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13405 Pfam ID:PF05046
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L50, mi
Gene (Uniprot):MRPL50
Chain IDs:OA (auth: h)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N5N7 Pfam ID:PF10501
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L51, mi
Gene (Uniprot):MRPL51
Chain IDs:PA (auth: i)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q4U2R6 Pfam ID:PF10244
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L52, mi
Gene (Uniprot):MRPL52
Chain IDs:QA (auth: j)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q86TS9 Pfam ID:PF18699
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L53, mi
Gene (Uniprot):MRPL53
Chain IDs:RA (auth: k)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EL3 Pfam ID:PF10780
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L54, mi
Gene (Uniprot):MRPL54
Chain IDs:SA (auth: l)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P161 Pfam ID:PF08561
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L55, mi
Gene (Uniprot):MRPL55
Chain IDs:TA (auth: m)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z7F7 Pfam ID:PF09776
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein 63, mitocho
Gene (Uniprot):MRPL57
Chain IDs:UA (auth: o)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BQC6 Pfam ID:PF14978
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptidyl-tRNA hydrolase ICT1,
Gene (Uniprot):MRPL58
Chain IDs:VA (auth: p)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q14197 Pfam ID:PF00472 EC:3.1.1.29
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Growth arrest and DNA damage-
Gene (Uniprot):GADD45GIP1
Chain IDs:WA (auth: q)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TAE8 Pfam ID:PF10147
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S18a, m
Gene (Uniprot):MRPS18A
Chain IDs:XA (auth: r)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVS2 Pfam ID:PF01084
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S30, mi
Gene (Uniprot):MRPS30
Chain IDs:YA (auth: s)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NP92 Pfam ID:PF07147
Polymer Type:polypeptide(L)
Molecule:Unknown protein or protein ex
Chain IDs:ZA (auth: t)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial assembly of rib
Gene (Uniprot):MALSU1
Chain IDs:AB (auth: u)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EH3 Pfam ID:PF02410
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MIEF1 upstream open reading f
Gene (Uniprot):MIEF1
Chain IDs:BB (auth: v)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:L0R8F8 Pfam ID:PF05347
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitocho
Gene (Uniprot):NDUFAB1
Chain IDs:CB (auth: w)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O14561 Pfam ID:PF00550
Ligand Molecules
MG
PNS
ZN
Primary Citation
Structures of the human mitochondrial ribosome in native states of assembly.
Nat. Struct. Mol. Biol. 24 866 869 (2017)
PMID: 28892042 DOI: 10.1038/nsmb.3464

Abstact

Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to ∼3-Å resolution. Comparison of the structures reveals insights into the timing of rRNA folding and protein incorporation during the final steps of ribosomal maturation and the evolutionary adaptations that are required to preserve biogenesis after the structural diversification of mitoribosomes. Furthermore, the structures redefine the ribosome silencing factor (RsfS) family as multifunctional biogenesis factors and identify two new assembly factors (L0R8F8 and mt-ACP) not previously implicated in mitoribosomal biogenesis.

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Protein

Chemical

Disease

Primary Citation of related structures
5OOM
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