› 5ool

Electron Microscopy
3.06Å resolution

Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA

Released:
DOI: 10.2210/pdb5ool/pdb
PDB 5ool coloured by chain and viewed from the front.
PDB 5ool coloured by chain and viewed from the side.
PDB 5ool coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Structures of the human mitochondrial ribosome in native states of assembly.
Brown A, Rathore S, Kimanius D, Aibara S, Bai XC, Rorbach J, Amunts A, Ramakrishnan V
Nat Struct Mol Biol 24 866-869 (2017)
PMID: 28892042
Related structures: EMD-3842

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 56-mer (preferred)
Entry contents:
54 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (56 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
Structure domains: Ribosomal Protein L4; Chain: A;
39S ribosomal protein L9, mitochondrial Chain: H
Molecule details ›
Chain: 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
Structure domains: Alpha-Beta Plaits
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:
Structure 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
Structure 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
Structure domains: Ribosomal protein L14
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
39S ribosomal protein L18, mitochondrial Chain: P
Molecule details ›
Chain: P
Length: 180 amino acids
Theoretical weight: 20.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H0U6 (Residues: 1-180; Coverage: 100%)
Gene names: HSPC071, MRPL18
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Structure domains: Ribosomal protein S11
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: 206 amino acids
Theoretical weight: 23.68 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NWU5 (Residues: 1-206; Coverage: 100%)
Gene names: HSPC158, MRPL22, MRPL25, RPML25
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
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
Structure domains: Alpha-Beta Plaits
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
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
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
Structure 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
Structure domains: Helix Hairpins
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
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
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: 215 amino acids
Theoretical weight: 23.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N983 (Residues: 1-215; Coverage: 100%)
Gene name: MRPL43
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Structure domains: Glutaredoxin
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: 212 amino acids
Theoretical weight: 23.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96GC5 (Residues: 1-212; Coverage: 100%)
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)
Structure domains: SUI1-like domain
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: 13.68 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q86TS9 (Residues: 1-123; Coverage: 100%)
Gene name: MRPL52
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
Structure domains: Glutaredoxin
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
Structure 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
Structure 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 or 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
Mitochondrial ribosome and complex I assembly factor AltMIEF1 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 names: AltMIEF1, AltMiD51, 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
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1559 nucleotides
Theoretical weight: 500.02 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
mitochondrial tRNAVal Chain: B
Molecule details ›
Chain: B
Length: 69 nucleotides
Theoretical weight: 22.02 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 92 x MG
Ligand ZN 3 x ZN
Ligand PNS 1 x PNS
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.06Å
Relevant EMDB volumes: EMD-3842

Quick links

Citations

16 review citations

Maintaining mitochondrial ribosome function: The role of ribosome rescue and recycling factors.
Nadler et al. (2022)
15 more

10 mentions without citation

Impact of Mitochondrial Fatty Acid Synthesis on Mitochondrial Biogenesis.
Nowinski et al. (2018)
9 more