› 6gb2

Electron Microscopy
3.2Å resolution

Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 39S ribosomal subunit.

Released:
DOI: 10.2210/pdb6gb2/pdb
PDB entry 6gb2 coloured by chain, front view.
PDB entry 6gb2 coloured by chain, side view.
PDB entry 6gb2 coloured by chain, top view.
Source organisms:
Primary publication:
Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM.
Kummer E, Leibundgut M, Rackham O, Lee RG, Boehringer D, Filipovska A, Ban N
Nature 560 263-267 (2018)
PMID: 30089917
Related structures: EMD-4370

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 62-mer (preferred)
PDBe Complex ID:
PDB-CPX-236649 (preferred)
Entry contents:
53 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (56 distinct):
39S ribosomal protein L12, mitochondrial Chains: BL, CL, DL, EL, FL, GL, HL
Molecule details ›
Chains: BL, CL, DL, EL, FL, GL, HL
Length: 198 amino acids
Theoretical weight: 21.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1U6S6 (Residues: 1-198; Coverage: 100%)
Gene name: MRPL12
Sequence domains:
39S ribosomal protein L27, mitochondrial Chain: B0
Molecule details ›
Chain: B0
Length: 148 amino acids
Theoretical weight: 15.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1U0F6 (Residues: 1-148; Coverage: 100%)
Gene name: MRPL27
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28m Chain: B1
Molecule details ›
Chain: B1
Length: 256 amino acids
Theoretical weight: 30.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZTW8 (Residues: 1-256; Coverage: 100%)
Gene name: MRPL28
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29m Chain: B2
Molecule details ›
Chain: B2
Length: 252 amino acids
Theoretical weight: 30.09 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SGC7 (Residues: 1-32, 33-250; Coverage: 100%)
Gene name: MRPL47
Sequence domains: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
Large ribosomal subunit protein uL30m Chain: B3
Molecule details ›
Chain: B3
Length: 161 amino acids
Theoretical weight: 18.59 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1MIP3 (Residues: 8-161; Coverage: 96%)
Gene name: MRPL30
Sequence domains: Ribosomal protein L30p/L7e
Mitochondrial ribosomal protein L55 Chain: B4
Molecule details ›
Chain: B4
Length: 126 amino acids
Theoretical weight: 15.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1ULI6 (Residues: 1-126; Coverage: 100%)
Gene name: MRPL55
Sequence domains: Mitochondrial ribosomal protein L55
Mitochondrial ribosomal protein L32 Chain: B5
Molecule details ›
Chain: B5
Length: 188 amino acids
Theoretical weight: 21.54 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein bL33m Chain: B6
Molecule details ›
Chain: B6
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TLP9 (Residues: 1-65; Coverage: 100%)
Gene name: MRPL33
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34m Chain: B7
Molecule details ›
Chain: B7
Length: 95 amino acids
Theoretical weight: 10.87 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1UFR4 (Residues: 1-95; Coverage: 100%)
Gene name: MRPL34
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35m Chain: B8
Molecule details ›
Chain: B8
Length: 188 amino acids
Theoretical weight: 21.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SVC5 (Residues: 1-79; Coverage: 83%)
Gene name: MRPL35
Ribosomal protein Chain: B9
Molecule details ›
Chain: B9
Length: 100 amino acids
Theoretical weight: 10.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287A731 (Residues: 1-100; Coverage: 100%)
Gene name: MRPL36
Sequence domains: Ribosomal protein L36
Translation initiation factor IF-2, mitochondrial Chain: BC
Molecule details ›
Chain: BC
Length: 657 amino acids
Theoretical weight: 72.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P46199 (Residues: 78-727; Coverage: 89%)
Gene name: MTIF2
Sequence domains:
Large ribosomal subunit protein uL2 RNA-binding domain-containing protein Chain: BD
Molecule details ›
Chain: BD
Length: 306 amino acids
Theoretical weight: 33.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RRN2 (Residues: 1-216; Coverage: 96%)
Gene name: MRPL2
Sequence domains: Ribosomal Proteins L2, RNA binding domain
ICT1 Chain: BE
Molecule details ›
Chain: BE
Length: 348 amino acids
Theoretical weight: 38.43 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein uL4m Chain: BF
Molecule details ›
Chain: BF
Length: 294 amino acids
Theoretical weight: 33.25 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287B9C4 (Residues: 1-250; Coverage: 92%)
Gene name: MRPL4
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein bL9m Chain: BI
Molecule details ›
Chain: BI
Length: 268 amino acids
Theoretical weight: 30.37 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LR45 (Residues: 1-268; Coverage: 100%)
Gene name: MRPL9
Sequence domains: Ribosomal protein L9, N-terminal domain
Large ribosomal subunit protein uL10m Chain: BJ
Molecule details ›
Chain: BJ
Length: 262 amino acids
Theoretical weight: 29.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RWJ0 (Residues: 10-257; Coverage: 97%)
Gene name: MRPL10
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein uL11m Chain: BK
Molecule details ›
Chain: BK
Length: 192 amino acids
Theoretical weight: 20.81 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RU54 (Residues: 1-41, 42-160; Coverage: 100%)
Gene name: MRPL11
Sequence domains: Ribosomal protein L11, RNA binding domain
Mitochondrial ribosomal protein L13 Chain: BN
Molecule details ›
Chain: BN
Length: 178 amino acids
Theoretical weight: 20.63 KDa
Source organism: Sus scrofa
Mitochondrial ribosomal protein L14 Chain: BO
Molecule details ›
Chain: BO
Length: 145 amino acids
Theoretical weight: 15.96 KDa
Source organism: Sus scrofa
Mitochondrial ribosomal protein L15 Chain: BP
Molecule details ›
Chain: BP
Length: 296 amino acids
Theoretical weight: 33.48 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein uL16m Chain: BQ
Molecule details ›
Chain: BQ
Length: 251 amino acids
Theoretical weight: 28.68 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RI89 (Residues: 1-251; Coverage: 100%)
Gene name: MRPL16
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17m Chain: BR
Molecule details ›
Chain: BR
Length: 169 amino acids
Theoretical weight: 19.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RMQ4 (Residues: 1-169; Coverage: 100%)
Gene name: MRPL17
Sequence domains: Ribosomal protein L17
Mitochondrial ribosomal protein L18 Chain: BS
Molecule details ›
Chain: BS
Length: 180 amino acids
Theoretical weight: 20.58 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZNK1 (Residues: 26-166; Coverage: 80%)
Gene name: MRPL18
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Mitochondrial ribosomal protein L19 Chain: BT
Molecule details ›
Chain: BT
Length: 292 amino acids
Theoretical weight: 33.44 KDa
Source organism: Sus scrofa
39S ribosomal protein L20, mitochondrial isoform 1 Chain: BU
Molecule details ›
Chain: BU
Length: 149 amino acids
Theoretical weight: 17.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZU56 (Residues: 1-149; Coverage: 100%)
Gene name: MRPL20
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21m Chain: BV
Molecule details ›
Chain: BV
Length: 209 amino acids
Theoretical weight: 23.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RY70 (Residues: 1-209; Coverage: 100%)
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22m Chain: BW
Molecule details ›
Chain: BW
Length: 210 amino acids
Theoretical weight: 24.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TXR4 (Residues: 1-210; Coverage: 100%)
Gene name: MRPL22
Sequence domains: Ribosomal protein L22p/L17e
Mitochondrial ribosomal protein L23 Chain: BX
Molecule details ›
Chain: BX
Length: 150 amino acids
Theoretical weight: 17.64 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein uL24m Chain: BY
Molecule details ›
Chain: BY
Length: 216 amino acids
Theoretical weight: 24.89 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RHJ1 (Residues: 1-216; Coverage: 100%)
Gene name: MRPL24
Sequence domains:
Large ribosomal subunit protein mL37 Chain: Ba
Molecule details ›
Chain: Ba
Length: 423 amino acids
Theoretical weight: 47.92 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BIV6 (Residues: 1-423; Coverage: 100%)
Gene name: MRPL37
Sequence domains: Mitochondrial 28S ribosomal protein S30 (PDCD9)
Large ribosomal subunit protein mL38 Chain: Bb
Molecule details ›
Chain: Bb
Length: 380 amino acids
Theoretical weight: 44.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RW03 (Residues: 1-380; Coverage: 100%)
Gene name: MRPL38
Sequence domains: Phosphatidylethanolamine-binding protein
TGS domain-containing protein Chain: Bc
Molecule details ›
Chain: Bc
Length: 334 amino acids
Theoretical weight: 38.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SHP6 (Residues: 1-303, 304-318; Coverage: 100%)
Gene name: MRPL39
Large ribosomal subunit protein mL40 Chain: Bd
Molecule details ›
Chain: Bd
Length: 206 amino acids
Theoretical weight: 24.08 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZP98 (Residues: 1-162; Coverage: 100%)
Gene name: MRPL40
Sequence domains: Mitochondrial ribosomal protein L28
39S ribosomal protein L41, mitochondrial Chain: Be
Molecule details ›
Chain: Be
Length: 135 amino acids
Theoretical weight: 15.07 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1F1K9 (Residues: 1-135; Coverage: 100%)
Gene name: MRPL41
Sequence domains: Mitochondrial ribosomal protein L27
Large ribosomal subunit protein mL42 Chain: Bf
Molecule details ›
Chain: Bf
Length: 142 amino acids
Theoretical weight: 16.68 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BQA1 (Residues: 1-142; Coverage: 100%)
Gene name: MRPL42
Sequence domains: Mitochondrial 28S ribosomal protein S32
Large ribosomal subunit protein mL43 Chain: Bg
Molecule details ›
Chain: Bg
Length: 159 amino acids
Theoretical weight: 17.73 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S8U4 (Residues: 1-159; Coverage: 100%)
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Large ribosomal subunit protein mL44 Chain: Bh
Molecule details ›
Chain: Bh
Length: 332 amino acids
Theoretical weight: 37.53 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SR64 (Residues: 1-332; Coverage: 100%)
Gene name: MRPL44
Large ribosomal subunit protein mL45 Chain: Bi
Molecule details ›
Chain: Bi
Length: 306 amino acids
Theoretical weight: 35.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGM5 (Residues: 1-306; Coverage: 100%)
Gene name: MRPL45
Sequence domains: Tim44-like domain
Large ribosomal subunit protein mL46 Chain: Bj
Molecule details ›
Chain: Bj
Length: 279 amino acids
Theoretical weight: 32.22 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SRT0 (Residues: 1-279; Coverage: 100%)
Gene name: MRPL46
Sequence domains: 39S mitochondrial ribosomal protein L46
Small ribosomal subunit protein uS10 domain-containing protein Chain: Bk
Molecule details ›
Chain: Bk
Length: 212 amino acids
Theoretical weight: 23.75 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480J9Z6 (Residues: 58-269; Coverage: 79%)
Gene name: MRPL48
Sequence domains: Ribosomal protein S10p/S20e
Large ribosomal subunit protein mL49 Chain: Bl
Molecule details ›
Chain: Bl
Length: 166 amino acids
Theoretical weight: 18.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0R4J8D6 (Residues: 1-122, 123-129; Coverage: 94%)
Gene name: MRPL49
Sequence domains: Mitochondrial large subunit ribosomal protein (Img2)
Large ribosomal subunit protein mL50 Chain: Bm
Molecule details ›
Chain: Bm
Length: 159 amino acids
Theoretical weight: 18.35 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3L9H6 (Residues: 40-198; Coverage: 80%)
Gene name: MRPL50
Sequence domains: Ribosomal subunit 39S
Large ribosomal subunit protein mL51 Chain: Bn
Molecule details ›
Chain: Bn
Length: 128 amino acids
Theoretical weight: 15.25 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1P1C8 (Residues: 1-128; Coverage: 100%)
Gene name: MRPL51
Sequence domains: Mitochondrial ribosomal subunit
Large ribosomal subunit protein mL52 Chain: Bo
Molecule details ›
Chain: Bo
Length: 124 amino acids
Theoretical weight: 13.81 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S9B7 (Residues: 38-47, 48-160; Coverage: 77%)
Gene name: MRPL52
Sequence domains: Mitoribosomal protein mL52
mL53, MRPL53 Chain: Bp
Molecule details ›
Chain: Bp
Length: 112 amino acids
Theoretical weight: 12.02 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein mL54 Chain: Bq
Molecule details ›
Chain: Bq
Length: 138 amino acids
Theoretical weight: 15.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LN63 (Residues: 1-160; Coverage: 86%)
Gene name: MRPL54
Sequence domains: Mitochondrial ribosomal protein L37
Mitochondrial ribosomal protein L57 Chain: Bt
Molecule details ›
Chain: Bt
Length: 102 amino acids
Theoretical weight: 12 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BP93 (Residues: 1-102; Coverage: 100%)
Gene name: MRPL57
Sequence domains: Mitochondrial ribosome protein 63
Large ribosomal subunit protein mL62 Chain: Bu
Molecule details ›
Chain: Bu
Length: 205 amino acids
Theoretical weight: 23.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZJR2 (Residues: 1-205; Coverage: 100%)
Gene name: MRPL58
Sequence domains: RF-1 domain
Large ribosomal subunit protein mL64 Chain: Bv
Molecule details ›
Chain: Bv
Length: 222 amino acids
Theoretical weight: 25.82 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZXA6 (Residues: 1-222; Coverage: 100%)
Gene name: GADD45GIP1
Sequence domains: Growth arrest and DNA-damage-inducible proteins-interacting protein 1
mL65, MRPS30 Chain: Bw
Molecule details ›
Chain: Bw
Length: 433 amino acids
Theoretical weight: 49.1 KDa
Source organism: Sus scrofa
Mitochondrial ribosomal protein S18A Chain: Bx
Molecule details ›
Chain: Bx
Length: 196 amino acids
Theoretical weight: 22.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RRH6 (Residues: 9-25, 26-181; Coverage: 95%)
Gene name: MRPS18A
Sequence domains: Ribosomal protein S18
unassigned secondary structure elements Chain: Bz
Molecule details ›
Chain: Bz
Length: 82 amino acids
Theoretical weight: 5.85 KDa
Source organism: Sus scrofa
16S ribosomal RNA, mitochondrial Chain: BA
Molecule details ›
Chain: BA
Length: 1571 nucleotides
Theoretical weight: 504.85 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
CP tRNAPhe, mitochondrial Chain: BB
Molecule details ›
Chain: BB
Length: 73 nucleotides
Theoretical weight: 23.4 KDa
Sequence domains: tRNA
P-site fMet-tRNAMet, mitochondrial Chain: AV
Molecule details ›
Chain: AV
Length: 71 nucleotides
Theoretical weight: 22.66 KDa

Ligands and Environments

7 bound ligands:
Ligand MG 216 x MG
Ligand ZN 3 x ZN
Ligand 5GP 2 x 5GP
Ligand SPM 2 x SPM
Ligand GSP 1 x GSP
Ligand NA 1 x NA
Ligand FME 1 x FME
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-4370
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Transport of Proteins into Mitochondria.
Hansen et al. (2019)
13 more