› 7oic

Electron Microscopy
3.1Å resolution

Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4

Released:
DOI: 10.2210/pdb7oic/pdb
PDB entry 7oic coloured by chain, front view.
PDB entry 7oic coloured by chain, side view.
PDB entry 7oic coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A distinct assembly pathway of the human 39S late pre-mitoribosome.
Cheng J, Berninghausen O, Beckmann R
OpenAccess logo Nat Commun 12 4544 (2021)
PMID: 34315873
Related structures: EMD-12925

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 57-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-251707 (preferred)
Entry contents:
55 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (57 distinct):
Large ribosomal subunit protein uL2m 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:
Large ribosomal subunit protein uL3m 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
Large ribosomal subunit protein uL4m 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
Large ribosomal subunit protein bL9m 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:
Large ribosomal subunit protein uL10m 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
Large ribosomal subunit protein uL11m 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:
Large ribosomal subunit protein uL13m 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
Large ribosomal subunit protein uL14m 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
Large ribosomal subunit protein uL15m 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
Large ribosomal subunit protein uL16m 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
Large ribosomal subunit protein bL17m 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
Large ribosomal subunit protein uL18m 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
Large ribosomal subunit protein bL19m 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
Large ribosomal subunit protein bL20m 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
Large ribosomal subunit protein bL21m 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
Large ribosomal subunit protein uL22m 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
Large ribosomal subunit protein uL23m 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
Large ribosomal subunit protein uL24m 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:
Large ribosomal subunit protein bL27m 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
Large ribosomal subunit protein bL28m Chain: X
Molecule details ›
Chain: X
Length: 256 amino acids
Theoretical weight: 30.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13084 (Residues: 1-256; Coverage: 100%)
Gene names: MAAT1, MRPL28
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29m 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)
Large ribosomal subunit protein uL30m 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
Large ribosomal subunit protein bL32m 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
Large ribosomal subunit protein bL33m 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
Large ribosomal subunit protein bL34m 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
Large ribosomal subunit protein bL35m 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
Large ribosomal subunit protein bL36m 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
Large ribosomal subunit protein mL37 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)
Large ribosomal subunit protein mL38 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
Large ribosomal subunit protein mL39 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
Large ribosomal subunit protein mL40 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
Large ribosomal subunit protein mL41 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
Large ribosomal subunit protein mL42 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
Large ribosomal subunit protein mL43 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
Large ribosomal subunit protein mL44 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
Sequence domains:
Large ribosomal subunit protein mL45 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
Large ribosomal subunit protein mL46 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
Large ribosomal subunit protein mL48 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
Large ribosomal subunit protein mL49 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)
Large ribosomal subunit protein mL50 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
Large ribosomal subunit protein mL51 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
Large ribosomal subunit protein mL52 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
Large ribosomal subunit protein mL53 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
Large ribosomal subunit protein mL54 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
Large ribosomal subunit protein mL55 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
Large ribosomal subunit protein mL63 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
Large ribosomal subunit protein mL62 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
Large ribosomal subunit protein mL64 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
Large ribosomal subunit protein mL66 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
Large ribosomal subunit protein mL65 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)
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
5-cytosine rRNA methyltransferase NSUN4 Chain: x
Molecule details ›
Chain: x
Length: 384 amino acids
Theoretical weight: 43.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96CB9 (Residues: 1-384; Coverage: 100%)
Gene name: NSUN4
Sequence domains: 16S rRNA methyltransferase RsmB/F
Transcription termination factor 4, mitochondrial Chain: y
Molecule details ›
Chain: y
Length: 381 amino acids
Theoretical weight: 44.01 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7Z6M4 (Residues: 1-381; Coverage: 100%)
Gene names: HSPC096, MTERF4, MTERFD2
Sequence domains: mTERF
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1559 nucleotides
Theoretical weight: 500.04 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
mitochondrial Val tRNA Chain: B
Molecule details ›
Chain: B
Length: 69 nucleotides
Theoretical weight: 22.02 KDa
Sequence domains: tRNA

Ligands and Environments

6 bound ligands:
Ligand MG 76 x MG
Ligand C 1 x C
Ligand A 1 x A
Ligand ZN 3 x ZN
Ligand PNS 1 x PNS
Ligand SAM 1 x SAM
1 modified residue:
Ligand MSE 1 x MSE

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-12925

Quick links

Citations

5 review citations

5-methylcytosine RNA methyltransferases and their potential roles in cancer.
Li et al. (2022)
4 more