› 7qh7

Electron Microscopy
2.89Å resolution

Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4

Released:
DOI: 10.2210/pdb7qh7/pdb
PDB entry 7qh7 coloured by chain, front view.
PDB entry 7qh7 coloured by chain, side view.
PDB entry 7qh7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit.
Rebelo-Guiomar P, Pellegrino S, Dent KC, Sas-Chen A, Miller-Fleming L, Garone C, Van Haute L, Rogan JF, Dinan A, Firth AE, Andrews B, Whitworth AJ, Schwartz S, Warren AJ, Minczuk M
Nat Commun 13 929 (2022)
PMID: 35177605
Related structures: EMD-13967

Function and Biology Details

Reaction catalysed: 
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 49-mer (preferred)
PDBe Complex ID:
PDB-CPX-125781 (preferred)
Entry contents:
47 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (49 distinct):
Large ribosomal subunit protein uL2m Chain: D
Molecule details ›
Chain: D
Length: 215 amino acids
Theoretical weight: 23.83 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q5T653 (Residues: 61-275; Coverage: 71%)
Gene names: CGI-22, MRPL2
Sequence domains:
Large ribosomal subunit protein uL3m Chain: E
Molecule details ›
Chain: E
Length: 304 amino acids
Theoretical weight: 34.02 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09001 (Residues: 45-348; Coverage: 87%)
Gene names: MRL3, MRPL3, RPML3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4m Chain: F
Molecule details ›
Chain: F
Length: 250 amino acids
Theoretical weight: 28.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYD3 (Residues: 45-294; Coverage: 80%)
Gene names: CDABP0091, CGI-28, MRPL4
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein bL9m Chain: H
Molecule details ›
Chain: H
Length: 95 amino acids
Theoretical weight: 11.13 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYD2 (Residues: 53-147; Coverage: 36%)
Gene name: MRPL9
Sequence domains: Ribosomal protein L9, N-terminal domain
Large ribosomal subunit protein uL10m Chain: I
Molecule details ›
Chain: I
Length: 30 amino acids
Theoretical weight: 3.55 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7Z7H8 (Residues: 37-66; Coverage: 12%)
Gene names: MRPL10, MRPL8, RPML8
Large ribosomal subunit protein uL13m Chain: K
Molecule details ›
Chain: K
Length: 177 amino acids
Theoretical weight: 20.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYD1 (Residues: 2-178; Coverage: 99%)
Gene name: MRPL13
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14m Chain: L
Molecule details ›
Chain: L
Length: 115 amino acids
Theoretical weight: 12.71 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P1L8 (Residues: 31-145; Coverage: 79%)
Gene names: MRPL14, MRPL32, RPML32
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15m Chain: M
Molecule details ›
Chain: M
Length: 287 amino acids
Theoretical weight: 32.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P015 (Residues: 10-296; Coverage: 97%)
Gene names: HSPC145, MRPL15
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16m Chain: N
Molecule details ›
Chain: N
Length: 201 amino acids
Theoretical weight: 23.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NX20 (Residues: 51-251; Coverage: 80%)
Gene names: MRPL16, PNAS-111
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17m Chain: O
Molecule details ›
Chain: O
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NRX2 (Residues: 9-160; Coverage: 87%)
Gene names: LIP2, MRPL17
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18m Chain: P
Molecule details ›
Chain: P
Length: 141 amino acids
Theoretical weight: 16.34 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H0U6 (Residues: 39-179; Coverage: 78%)
Gene names: HSPC071, MRPL18
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19m Chain: Q
Molecule details ›
Chain: Q
Length: 217 amino acids
Theoretical weight: 25.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49406 (Residues: 74-290; Coverage: 74%)
Gene names: KIAA0104, MRPL15, MRPL19
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20m Chain: R
Molecule details ›
Chain: R
Length: 139 amino acids
Theoretical weight: 16.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYC9 (Residues: 10-148; Coverage: 93%)
Gene name: MRPL20
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21m Chain: S
Molecule details ›
Chain: S
Length: 156 amino acids
Theoretical weight: 17.79 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7Z2W9 (Residues: 49-204; Coverage: 76%)
Gene name: MRPL21
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22m Chain: T
Molecule details ›
Chain: T
Length: 166 amino acids
Theoretical weight: 19.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NWU5 (Residues: 41-206; Coverage: 81%)
Gene names: HSPC158, MRPL22, MRPL25, RPML25
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23m Chain: U
Molecule details ›
Chain: U
Length: 125 amino acids
Theoretical weight: 14.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q16540 (Residues: 2-153; Coverage: 82%)
Gene names: L23MRP, MRPL23, RPL23L
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24m Chain: V
Molecule details ›
Chain: V
Length: 48 amino acids
Theoretical weight: 5.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96A35 (Residues: 169-216; Coverage: 22%)
Gene name: MRPL24
Large ribosomal subunit protein bL27m Chain: W
Molecule details ›
Chain: W
Length: 100 amino acids
Theoretical weight: 11.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P0M9 (Residues: 49-148; Coverage: 68%)
Gene names: HSPC250, MRPL27
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28m Chain: X
Molecule details ›
Chain: X
Length: 243 amino acids
Theoretical weight: 28.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13084 (Residues: 2-244; Coverage: 95%)
Gene names: MAAT1, MRPL28
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29m Chain: Y
Molecule details ›
Chain: Y
Length: 175 amino acids
Theoretical weight: 21.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9HD33 (Residues: 63-237; Coverage: 70%)
Gene names: CGI-204, MRPL47, NCM1
Sequence domains: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
Large ribosomal subunit protein uL30m Chain: Z
Molecule details ›
Chain: Z
Length: 115 amino acids
Theoretical weight: 13.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8TCC3 (Residues: 35-149; Coverage: 71%)
Gene names: HSPC249, MRPL28, MRPL30, RPML28
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32m Chain: 0
Molecule details ›
Chain: 0
Length: 108 amino acids
Theoretical weight: 12.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYC8 (Residues: 79-186; Coverage: 57%)
Gene names: HSPC283, MRPL32
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33m Chain: 1
Molecule details ›
Chain: 1
Length: 49 amino acids
Theoretical weight: 5.83 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75394 (Residues: 14-62; Coverage: 75%)
Gene names: C2orf1, MRPL33
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34m Chain: 2
Molecule details ›
Chain: 2
Length: 45 amino acids
Theoretical weight: 5.24 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BQ48 (Residues: 48-92; Coverage: 49%)
Gene name: MRPL34
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35m Chain: 3
Molecule details ›
Chain: 3
Length: 95 amino acids
Theoretical weight: 11.79 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NZE8 (Residues: 94-188; Coverage: 51%)
Gene names: BM-007, MRPL35
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein mL37 Chain: 5
Molecule details ›
Chain: 5
Length: 392 amino acids
Theoretical weight: 45.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BZE1 (Residues: 31-422; Coverage: 93%)
Gene names: HSPC235, MRPL2, MRPL37, RPML2
Sequence domains: Mitochondrial 28S ribosomal protein S30 (PDCD9)
Large ribosomal subunit protein mL38 Chain: 6
Molecule details ›
Chain: 6
Length: 292 amino acids
Theoretical weight: 34.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96DV4 (Residues: 27-380; Coverage: 77%)
Gene names: HSPC262, MRPL38
Sequence domains: Phosphatidylethanolamine-binding protein
Large ribosomal subunit protein mL39 Chain: 7
Molecule details ›
Chain: 7
Length: 287 amino acids
Theoretical weight: 33.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NYK5 (Residues: 36-322; Coverage: 85%)
Gene names: C21orf92, MRPL39, MRPL5, MSTP003, PRED22, RPML5
Large ribosomal subunit protein mL41 Chain: 9
Molecule details ›
Chain: 9
Length: 123 amino acids
Theoretical weight: 14.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8IXM3 (Residues: 15-137; Coverage: 90%)
Gene names: BMRP, MRPL27, MRPL41, PIG3, RPML27
Sequence domains: Mitochondrial ribosomal protein L27
Large ribosomal subunit protein mL42 Chain: a
Molecule details ›
Chain: a
Length: 80 amino acids
Theoretical weight: 9.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y6G3 (Residues: 39-142; Coverage: 56%)
Gene names: HSPC204, MRPL31, MRPL42, MRPS32, PTD007, RPML31
Sequence domains: Mitochondrial 28S ribosomal protein S32
Large ribosomal subunit protein mL43 Chain: b
Molecule details ›
Chain: b
Length: 148 amino acids
Theoretical weight: 16.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N983 (Residues: 2-149; Coverage: 69%)
Gene name: MRPL43
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Large ribosomal subunit protein mL44 Chain: c
Molecule details ›
Chain: c
Length: 287 amino acids
Theoretical weight: 32.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H9J2 (Residues: 31-317; Coverage: 86%)
Gene name: MRPL44
Sequence domains:
Large ribosomal subunit protein mL45 Chain: d
Molecule details ›
Chain: d
Length: 169 amino acids
Theoretical weight: 19.85 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BRJ2 (Residues: 117-285; Coverage: 55%)
Gene name: MRPL45
Sequence domains: Tim44-like domain
Large ribosomal subunit protein mL48 Chain: f
Molecule details ›
Chain: f
Length: 17 amino acids
Theoretical weight: 2.02 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96GC5 (Residues: 48-64; Coverage: 8%)
Gene names: CGI-118, HSPC290, MRPL48
Large ribosomal subunit protein mL49 Chain: g
Molecule details ›
Chain: g
Length: 129 amino acids
Theoretical weight: 15.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13405 (Residues: 38-166; Coverage: 78%)
Gene names: C11orf4, MRPL49, NOF1, OK/SW-cl.67
Sequence domains: Mitochondrial large subunit ribosomal protein (Img2)
Large ribosomal subunit protein mL50 Chain: h
Molecule details ›
Chain: h
Length: 105 amino acids
Theoretical weight: 12.11 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N5N7 (Residues: 53-157; Coverage: 67%)
Gene name: MRPL50
Sequence domains: Ribosomal subunit 39S
Large ribosomal subunit protein mL51 Chain: i
Molecule details ›
Chain: i
Length: 97 amino acids
Theoretical weight: 11.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q4U2R6 (Residues: 32-128; Coverage: 76%)
Gene names: CDA09, HSPC241, MRP64, MRPL51
Sequence domains: Mitochondrial ribosomal subunit
Large ribosomal subunit protein mL52 Chain: j
Molecule details ›
Chain: j
Length: 86 amino acids
Theoretical weight: 9.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q86TS9 (Residues: 23-108; Coverage: 70%)
Gene name: MRPL52
Sequence domains: Mitoribosomal protein mL52
Large ribosomal subunit protein mL63 Chain: o
Molecule details ›
Chain: o
Length: 81 amino acids
Theoretical weight: 9.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BQC6 (Residues: 22-102; Coverage: 79%)
Gene names: MRP63, MRPL57
Sequence domains: Mitochondrial ribosome protein 63
Large ribosomal subunit protein mL62 Chain: p
Molecule details ›
Chain: p
Length: 125 amino acids
Theoretical weight: 14.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14197 (Residues: 38-193; Coverage: 61%)
Gene names: DS1, ICT1, MRPL58
Sequence domains: RF-1 domain
Large ribosomal subunit protein mL64 Chain: q
Molecule details ›
Chain: q
Length: 101 amino acids
Theoretical weight: 11.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8TAE8 (Residues: 25-125; Coverage: 46%)
Gene names: GADD45GIP1, MRPL59, PLINP1, PRG6
Sequence domains: Growth arrest and DNA-damage-inducible proteins-interacting protein 1
Large ribosomal subunit protein mL66 Chain: r
Molecule details ›
Chain: r
Length: 140 amino acids
Theoretical weight: 16.35 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NVS2 (Residues: 57-196; Coverage: 71%)
Gene name: MRPS18A
Sequence domains: Ribosomal protein S18
Large ribosomal subunit protein mL65 Chain: s
Molecule details ›
Chain: s
Length: 390 amino acids
Theoretical weight: 45.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NP92 (Residues: 41-430; Coverage: 89%)
Gene names: BM-047, MRPS30, PDCD9
Sequence domains: Mitochondrial 28S ribosomal protein S30 (PDCD9)
Mitochondrial assembly of ribosomal large subunit protein 1 Chain: u
Molecule details ›
Chain: u
Length: 111 amino acids
Theoretical weight: 13.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96EH3 (Residues: 91-201; Coverage: 47%)
Gene names: C7orf30, MALSU1
Sequence domains: Ribosomal silencing factor during starvation
Mitochondrial ribosome and complex I assembly factor AltMIEF1 Chain: v
Molecule details ›
Chain: v
Length: 69 amino acids
Theoretical weight: 8.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: L0R8F8 (Residues: 2-70; Coverage: 99%)
Gene names: AltMIEF1, AltMiD51, MIEF1
Sequence domains: Complex 1 protein (LYR family)
Acyl carrier protein, mitochondrial Chain: w
Molecule details ›
Chain: w
Length: 79 amino acids
Theoretical weight: 9.14 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O14561 (Residues: 74-152; Coverage: 51%)
Gene name: NDUFAB1
Sequence domains: Phosphopantetheine attachment site
Large ribosomal subunit protein bL36m Chain: 4
Molecule details ›
Chain: 4
Length: 37 amino acids
Theoretical weight: 4.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P0J6 (Residues: 66-102; Coverage: 36%)
Gene names: BRIP1, MRPL36
Sequence domains: Ribosomal protein L36
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1256 nucleotides
Theoretical weight: 403.06 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
mitochondrial tRNAVal Chain: B
Molecule details ›
Chain: B
Length: 61 nucleotides
Theoretical weight: 19.53 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 50 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.89Å
Relevant EMDB volumes: EMD-13967

Quick links

Citations

1 review citation

Modopathies Caused by Mutations in Genes Encoding for Mitochondrial RNA Modifying Enzymes: Molecular Mechanisms and Yeast Disease Models.
Magistrati et al. (2023)
6 other articles