› 7a5j

Electron Microscopy
3.1Å resolution

Structure of the split human mitoribosomal large subunit with P-and E-site mt-tRNAs

Released:
DOI: 10.2210/pdb7a5j/pdb
PDB 7a5j coloured by chain and viewed from the front.
PDB 7a5j coloured by chain and viewed from the side.
PDB 7a5j coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Elongational stalling activates mitoribosome-associated quality control.
Desai N, Yang H, Chandrasekaran V, Kazi R, Minczuk M, Ramakrishnan V
Science 370 1105-1110 (2020)
PMID: 33243891
Related structures: EMD-11645

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 63-mer (preferred)
Entry contents:
58 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (61 distinct):
39S ribosomal protein L2, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 305 amino acids
Theoretical weight: 33.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q5T653 (Residues: 1-305; Coverage: 100%)
Gene names: CGI-22, MRPL2
Sequence domains:
39S ribosomal protein L3, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 348 amino acids
Theoretical weight: 38.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09001 (Residues: 1-348; Coverage: 100%)
Gene names: MRL3, MRPL3, RPML3
Sequence domains: Ribosomal protein L3
39S ribosomal protein L4, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 311 amino acids
Theoretical weight: 34.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYD3 (Residues: 1-311; Coverage: 100%)
Gene names: CDABP0091, CGI-28, MRPL4
Sequence domains: Ribosomal protein L4/L1 family
39S ribosomal protein L9, mitochondrial Chains: C, H
Molecule details ›
Chains: C, H
Length: 267 amino acids
Theoretical weight: 30.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYD2 (Residues: 1-267; Coverage: 100%)
Gene name: MRPL9
Sequence domains: Ribosomal protein L9, N-terminal domain
39S ribosomal protein L10, mitochondrial Chain: I
Molecule details ›
Chain: I
Length: 261 amino acids
Theoretical weight: 29.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7Z7H8 (Residues: 1-261; Coverage: 100%)
Gene names: MRPL10, MRPL8, RPML8
Sequence domains: Ribosomal protein L10
39S ribosomal protein L11, mitochondrial Chain: J
Molecule details ›
Chain: J
Length: 192 amino acids
Theoretical weight: 20.72 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3B7 (Residues: 1-192; Coverage: 100%)
Gene names: CGI-113, MRPL11
Sequence domains:
39S ribosomal protein L13, mitochondrial Chain: K
Molecule details ›
Chain: K
Length: 178 amino acids
Theoretical weight: 20.72 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYD1 (Residues: 1-178; Coverage: 100%)
Gene name: MRPL13
Sequence domains: Ribosomal protein L13
39S ribosomal protein L14, mitochondrial Chain: L
Molecule details ›
Chain: L
Length: 145 amino acids
Theoretical weight: 15.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P1L8 (Residues: 1-145; Coverage: 100%)
Gene names: MRPL14, MRPL32, RPML32
Sequence domains: Ribosomal protein L14p/L23e
39S ribosomal protein L15, mitochondrial Chain: M
Molecule details ›
Chain: M
Length: 296 amino acids
Theoretical weight: 33.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P015 (Residues: 1-296; Coverage: 100%)
Gene names: HSPC145, MRPL15
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
39S ribosomal protein L16, mitochondrial Chain: N
Molecule details ›
Chain: N
Length: 251 amino acids
Theoretical weight: 28.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NX20 (Residues: 1-251; Coverage: 100%)
Gene names: MRPL16, PNAS-111
Sequence domains: Ribosomal protein L16p/L10e
39S ribosomal protein L17, mitochondrial Chain: O
Molecule details ›
Chain: O
Length: 175 amino acids
Theoretical weight: 20.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NRX2 (Residues: 1-175; Coverage: 100%)
Gene names: LIP2, MRPL17
Sequence domains: Ribosomal protein L17
Mitochondrial ribosomal protein L18, isoform CRA_b Chain: P
Molecule details ›
Chain: P
Length: 179 amino acids
Theoretical weight: 20.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: A8K9D2 (Residues: 1-179; Coverage: 100%)
Gene names: MRPL18, hCG_34030
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
39S ribosomal protein L19, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 292 amino acids
Theoretical weight: 33.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49406 (Residues: 1-292; Coverage: 100%)
Gene names: KIAA0104, MRPL15, MRPL19
Sequence domains: Ribosomal protein L19
39S ribosomal protein L20, mitochondrial Chain: R
Molecule details ›
Chain: R
Length: 149 amino acids
Theoretical weight: 17.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYC9 (Residues: 1-149; Coverage: 100%)
Gene name: MRPL20
Sequence domains: Ribosomal protein L20
39S ribosomal protein L21, mitochondrial Chain: S
Molecule details ›
Chain: S
Length: 205 amino acids
Theoretical weight: 22.85 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7Z2W9 (Residues: 1-205; Coverage: 100%)
Gene name: MRPL21
Sequence domains: Ribosomal prokaryotic L21 protein
39S ribosomal protein L22, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 212 amino acids
Theoretical weight: 24.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: E7ESL0 (Residues: 1-212; Coverage: 100%)
Gene name: MRPL22
Sequence domains: Ribosomal protein L22p/L17e
39S ribosomal protein L23, mitochondrial Chain: U
Molecule details ›
Chain: U
Length: 153 amino acids
Theoretical weight: 17.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q16540 (Residues: 1-153; Coverage: 100%)
Gene names: L23MRP, MRPL23, RPL23L
Sequence domains: Ribosomal protein L23
39S ribosomal protein L24, mitochondrial Chain: V
Molecule details ›
Chain: V
Length: 216 amino acids
Theoretical weight: 24.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96A35 (Residues: 1-216; Coverage: 100%)
Gene name: MRPL24
Sequence domains:
39S ribosomal protein L27, mitochondrial Chain: W
Molecule details ›
Chain: W
Length: 148 amino acids
Theoretical weight: 16.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P0M9 (Residues: 1-148; Coverage: 100%)
Gene names: HSPC250, MRPL27
Sequence domains: Ribosomal L27 protein
39S ribosomal protein L28, mitochondrial Chain: X
Molecule details ›
Chain: X
Length: 256 amino acids
Theoretical weight: 30.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13084 (Residues: 1-256; Coverage: 100%)
Gene names: MAAT1, MRPL28
Sequence domains: Ribosomal L28 family
39S ribosomal protein L47, mitochondrial Chain: Y
Molecule details ›
Chain: Y
Length: 250 amino acids
Theoretical weight: 29.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9HD33 (Residues: 1-250; Coverage: 100%)
Gene names: CGI-204, MRPL47, NCM1
Sequence domains: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
39S ribosomal protein L30, mitochondrial Chain: Z
Molecule details ›
Chain: Z
Length: 161 amino acids
Theoretical weight: 18.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8TCC3 (Residues: 1-161; Coverage: 100%)
Gene names: HSPC249, MRPL28, MRPL30, RPML28
Sequence domains: Ribosomal protein L30p/L7e
39S ribosomal protein L32, mitochondrial Chain: 0
Molecule details ›
Chain: 0
Length: 188 amino acids
Theoretical weight: 21.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYC8 (Residues: 1-188; Coverage: 100%)
Gene names: HSPC283, MRPL32
Sequence domains: Ribosomal L32p protein family
39S ribosomal protein L33, mitochondrial Chain: 1
Molecule details ›
Chain: 1
Length: 65 amino acids
Theoretical weight: 7.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75394 (Residues: 1-65; Coverage: 100%)
Gene names: C2orf1, MRPL33
Sequence domains: Ribosomal protein L33
39S ribosomal protein L34, mitochondrial Chain: 2
Molecule details ›
Chain: 2
Length: 92 amino acids
Theoretical weight: 10.18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BQ48 (Residues: 1-92; Coverage: 100%)
Gene name: MRPL34
Sequence domains: Ribosomal protein L34
39S ribosomal protein L35, mitochondrial Chain: 3
Molecule details ›
Chain: 3
Length: 188 amino acids
Theoretical weight: 21.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NZE8 (Residues: 1-188; Coverage: 100%)
Gene names: BM-007, MRPL35
Sequence domains: Ribosomal protein L35
39S ribosomal protein L36, mitochondrial Chain: 4
Molecule details ›
Chain: 4
Length: 103 amino acids
Theoretical weight: 11.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P0J6 (Residues: 1-103; Coverage: 100%)
Gene names: BRIP1, MRPL36
Sequence domains: Ribosomal protein L36
39S ribosomal protein L37, mitochondrial Chain: 5
Molecule details ›
Chain: 5
Length: 423 amino acids
Theoretical weight: 48.18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BZE1 (Residues: 1-423; Coverage: 100%)
Gene names: HSPC235, MRPL2, MRPL37, RPML2
Sequence domains: Mitochondrial 28S ribosomal protein S30 (PDCD9)
39S ribosomal protein L38, mitochondrial Chain: 6
Molecule details ›
Chain: 6
Length: 380 amino acids
Theoretical weight: 44.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96DV4 (Residues: 1-380; Coverage: 100%)
Gene names: HSPC262, MRPL38
Sequence domains: Phosphatidylethanolamine-binding protein
39S ribosomal protein L39, mitochondrial Chain: 7
Molecule details ›
Chain: 7
Length: 338 amino acids
Theoretical weight: 38.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NYK5 (Residues: 1-338; Coverage: 100%)
Gene names: C21orf92, MRPL39, MRPL5, MSTP003, PRED22, RPML5
39S ribosomal protein L40, mitochondrial Chain: 8
Molecule details ›
Chain: 8
Length: 206 amino acids
Theoretical weight: 24.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NQ50 (Residues: 1-206; Coverage: 100%)
Gene names: MRPL40, NLVCF, URIM
Sequence domains: Mitochondrial ribosomal protein L28
39S ribosomal protein L41, mitochondrial Chain: 9
Molecule details ›
Chain: 9
Length: 137 amino acids
Theoretical weight: 15.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8IXM3 (Residues: 1-137; Coverage: 100%)
Gene names: BMRP, MRPL27, MRPL41, PIG3, RPML27
Sequence domains: Mitochondrial ribosomal protein L27
39S ribosomal protein L42, mitochondrial Chain: a
Molecule details ›
Chain: a
Length: 142 amino acids
Theoretical weight: 16.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y6G3 (Residues: 1-142; Coverage: 100%)
Gene names: HSPC204, MRPL31, MRPL42, MRPS32, PTD007, RPML31
Sequence domains: Mitochondrial 28S ribosomal protein S32
39S ribosomal protein L43, mitochondrial Chain: b
Molecule details ›
Chain: b
Length: 155 amino acids
Theoretical weight: 17.45 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N983 (Residues: 1-155; Coverage: 72%)
Gene name: MRPL43
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
39S ribosomal protein L44, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 332 amino acids
Theoretical weight: 37.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H9J2 (Residues: 1-332; Coverage: 100%)
Gene name: MRPL44
39S ribosomal protein L45, mitochondrial Chain: d
Molecule details ›
Chain: d
Length: 306 amino acids
Theoretical weight: 35.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BRJ2 (Residues: 1-306; Coverage: 100%)
Gene name: MRPL45
Sequence domains: Tim44-like domain
39S ribosomal protein L46, mitochondrial Chain: e
Molecule details ›
Chain: e
Length: 279 amino acids
Theoretical weight: 31.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H2W6 (Residues: 1-279; Coverage: 100%)
Gene names: C15orf4, LIECG2, MRPL46
Sequence domains: 39S mitochondrial ribosomal protein L46
39S ribosomal protein L48, mitochondrial Chain: f
Molecule details ›
Chain: f
Length: 194 amino acids
Theoretical weight: 21.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96GC5 (Residues: 1-194; Coverage: 92%)
Gene names: CGI-118, HSPC290, MRPL48
Sequence domains: Ribosomal protein S10p/S20e
39S ribosomal protein L49, mitochondrial Chain: g
Molecule details ›
Chain: g
Length: 166 amino acids
Theoretical weight: 19.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13405 (Residues: 1-166; Coverage: 100%)
Gene names: C11orf4, MRPL49, NOF1, OK/SW-cl.67
Sequence domains: Mitochondrial large subunit ribosomal protein (Img2)
39S ribosomal protein L50, mitochondrial Chain: h
Molecule details ›
Chain: h
Length: 158 amino acids
Theoretical weight: 18.35 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N5N7 (Residues: 1-158; Coverage: 100%)
Gene name: MRPL50
Sequence domains: Ribosomal subunit 39S
39S ribosomal protein L51, mitochondrial Chain: i
Molecule details ›
Chain: i
Length: 128 amino acids
Theoretical weight: 15.13 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q4U2R6 (Residues: 1-128; Coverage: 100%)
Gene names: CDA09, HSPC241, MRP64, MRPL51
Sequence domains: Mitochondrial ribosomal subunit
39S ribosomal protein L52, mitochondrial Chain: j
Molecule details ›
Chain: j
Length: 123 amino acids
Theoretical weight: 13.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: A8K7J6 (Residues: 1-123; Coverage: 100%)
Sequence domains: Mitoribosomal protein mL52
39S ribosomal protein L53, mitochondrial Chain: k
Molecule details ›
Chain: k
Length: 112 amino acids
Theoretical weight: 12.13 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96EL3 (Residues: 1-112; Coverage: 100%)
Gene name: MRPL53
Sequence domains: 39S ribosomal protein L53/MRP-L53
39S ribosomal protein L54, mitochondrial Chain: l
Molecule details ›
Chain: l
Length: 138 amino acids
Theoretical weight: 15.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P161 (Residues: 1-138; Coverage: 100%)
Gene name: MRPL54
Sequence domains: Mitochondrial ribosomal protein L37
39S ribosomal protein L55, mitochondrial Chain: m
Molecule details ›
Chain: m
Length: 128 amino acids
Theoretical weight: 15.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7Z7F7 (Residues: 1-128; Coverage: 100%)
Gene names: MRPL55, UNQ5835/PRO19675
Sequence domains: Mitochondrial ribosomal protein L55
Ribosomal protein 63, mitochondrial Chain: o
Molecule details ›
Chain: o
Length: 102 amino acids
Theoretical weight: 12.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BQC6 (Residues: 1-102; Coverage: 100%)
Gene names: MRP63, MRPL57
Sequence domains: Mitochondrial ribosome protein 63
Peptidyl-tRNA hydrolase ICT1, mitochondrial Chain: p
Molecule details ›
Chain: p
Length: 206 amino acids
Theoretical weight: 23.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14197 (Residues: 1-206; Coverage: 100%)
Gene names: DS1, ICT1, MRPL58
Sequence domains: RF-1 domain
Growth arrest and DNA damage-inducible proteins-interacting protein 1 Chain: q
Molecule details ›
Chain: q
Length: 222 amino acids
Theoretical weight: 25.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8TAE8 (Residues: 1-222; Coverage: 100%)
Gene names: GADD45GIP1, MRPL59, PLINP1, PRG6
Sequence domains: Growth arrest and DNA-damage-inducible proteins-interacting protein 1
39S ribosomal protein S18a, mitochondrial Chain: r
Molecule details ›
Chain: r
Length: 196 amino acids
Theoretical weight: 22.22 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NVS2 (Residues: 1-196; Coverage: 100%)
Gene name: MRPS18A
Sequence domains: Ribosomal protein S18
39S ribosomal protein S30, mitochondrial Chain: s
Molecule details ›
Chain: s
Length: 439 amino acids
Theoretical weight: 50.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NP92 (Residues: 1-439; Coverage: 100%)
Gene names: BM-047, MRPS30, PDCD9
Sequence domains: Mitochondrial 28S ribosomal protein S30 (PDCD9)
Unknown protein/protein extension Chain: t
Molecule details ›
Chain: t
Length: 28 amino acids
Theoretical weight: 2.4 KDa
Source organism: Homo sapiens
Mitochondrial assembly of ribosomal large subunit protein 1 Chain: u
Molecule details ›
Chain: u
Length: 234 amino acids
Theoretical weight: 26.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96EH3 (Residues: 1-234; Coverage: 100%)
Gene names: C7orf30, MALSU1
Sequence domains: Ribosomal silencing factor during starvation
MIEF1 upstream open reading frame protein Chain: v
Molecule details ›
Chain: v
Length: 70 amino acids
Theoretical weight: 8.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: L0R8F8 (Residues: 1-70; Coverage: 100%)
Gene name: MIEF1
Sequence domains: Complex 1 protein (LYR family)
Acyl carrier protein, mitochondrial Chain: w
Molecule details ›
Chain: w
Length: 156 amino acids
Theoretical weight: 17.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O14561 (Residues: 1-156; Coverage: 100%)
Gene name: NDUFAB1
Sequence domains: Phosphopantetheine attachment site
50S ribosomal protein L1 Chain: n
Molecule details ›
Chain: n
Length: 229 amino acids
Theoretical weight: 24.87 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GV9 (Residues: 1-229; Coverage: 100%)
Gene names: TT_C1739, rplA
Sequence domains: Ribosomal protein L1p/L10e family
nascent chain Chain: Y2
Molecule details ›
Chain: Y2
Length: 29 amino acids
Theoretical weight: 2.49 KDa
Source organism: Homo sapiens
Unknown protein/protein extension Chain: y
Molecule details ›
Chain: y
Length: 32 amino acids
Theoretical weight: 2.74 KDa
Source organism: Homo sapiens
unknown protein/protein extension Chain: z
Molecule details ›
Chain: z
Length: 14 amino acids
Theoretical weight: 1.21 KDa
Source organism: Homo sapiens
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1559 nucleotides
Theoretical weight: 500.02 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
mt-tRNAVal Chain: B
Molecule details ›
Chain: B
Length: 69 nucleotides
Theoretical weight: 22.02 KDa
mt-tRNA Chains: G, x
Molecule details ›
Chains: G, x
Length: 73 nucleotides
Theoretical weight: 23.38 KDa
Sequence domains: tRNA

Ligands and Environments

5 bound ligands:
Ligand MG 92 x MG
Ligand ZN 3 x ZN
Ligand PNS 1 x PNS
Ligand CL 2 x CL
Ligand NA 4 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-11645

Quick links

Citations

1 review citation

Mechanisms and regulation of protein synthesis in mitochondria.
Kummer et al. (2021)