› 8oit

Electron Microscopy
2.9Å resolution

39S human mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA

Released:
DOI: 10.2210/pdb8oit/pdb
PDB entry 8oit coloured by chain, front view.
PDB entry 8oit coloured by chain, side view.
PDB entry 8oit coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of translation termination at noncanonical stop codons in human mitochondria.
Saurer M, Leibundgut M, Nadimpalli HP, Scaiola A, Schönhut T, Lee RG, Siira SJ, Rackham O, Dreos R, Lenarčič T, Kummer E, Gatfield D, Filipovska A, Ban N
Science 380 531-536 (2023)
PMID: 37141370
Related structures: EMD-16899

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 domain:

Structure analysis Details

Assembly composition:
hetero 62-mer (preferred)
PDBe Complex ID:
PDB-CPX-218035 (preferred)
Entry contents:
53 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (57 distinct):
Large ribosomal subunit protein bL12m Chains: B1, B2, B3, B4, B5, B6
Molecule details ›
Chains: B1, B2, B3, B4, B5, B6
Length: 198 amino acids
Theoretical weight: 21.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P52815 (Residues: 1-198; Coverage: 100%)
Gene names: MRPL12, MRPL7, RPML12
Sequence domains:
Large ribosomal subunit protein uL22m Chain: BA
Molecule details ›
Chain: BA
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: BB
Molecule details ›
Chain: BB
Length: 153 amino acids
Theoretical weight: 17.85 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: BC
Molecule details ›
Chain: BC
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: BD
Molecule details ›
Chain: BD
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: BE
Molecule details ›
Chain: BE
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
Large ribosomal subunit protein uL29m Chain: BF
Molecule details ›
Chain: BF
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: BG
Molecule details ›
Chain: BG
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: BH
Molecule details ›
Chain: BH
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: BI
Molecule details ›
Chain: BI
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: BJ
Molecule details ›
Chain: BJ
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: BK
Molecule details ›
Chain: BK
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 uL2m Chain: BL
Molecule details ›
Chain: BL
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: BM
Molecule details ›
Chain: BM
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: BN
Molecule details ›
Chain: BN
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: BO
Molecule details ›
Chain: BO
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: BP
Molecule details ›
Chain: BP
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: BQ
Molecule details ›
Chain: BQ
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: BR
Molecule details ›
Chain: BR
Length: 178 amino acids
Theoretical weight: 20.77 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: BS
Molecule details ›
Chain: BS
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: BT
Molecule details ›
Chain: BT
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: BU
Molecule details ›
Chain: BU
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: BV
Molecule details ›
Chain: BV
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: BW
Molecule details ›
Chain: BW
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: BX
Molecule details ›
Chain: BX
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: BY
Molecule details ›
Chain: BY
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: BZ
Molecule details ›
Chain: BZ
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 mL52 Chain: Ba
Molecule details ›
Chain: Ba
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: Bb
Molecule details ›
Chain: Bb
Length: 112 amino acids
Theoretical weight: 12.17 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: Bc
Molecule details ›
Chain: Bc
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: Bd
Molecule details ›
Chain: Bd
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: Be
Molecule details ›
Chain: Be
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: Bf
Molecule details ›
Chain: Bf
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: Bg
Molecule details ›
Chain: Bg
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: Bh
Molecule details ›
Chain: Bh
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: Bi
Molecule details ›
Chain: Bi
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)
Large ribosomal subunit protein uL1m Chain: Bj
Molecule details ›
Chain: Bj
Length: 325 amino acids
Theoretical weight: 36.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYD6 (Residues: 1-325; Coverage: 100%)
Gene names: BM-022, MRPL1
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein bL36m Chain: Bl
Molecule details ›
Chain: Bl
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: Bm
Molecule details ›
Chain: Bm
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: Bn
Molecule details ›
Chain: Bn
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: Bo
Molecule details ›
Chain: Bo
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: Bp
Molecule details ›
Chain: Bp
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: Bq
Molecule details ›
Chain: Bq
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: Br
Molecule details ›
Chain: Br
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: Bs
Molecule details ›
Chain: Bs
Length: 215 amino acids
Theoretical weight: 23.35 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N983 (Residues: 2-215; Coverage: 100%)
Gene name: MRPL43
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Large ribosomal subunit protein mL44 Chain: Bt
Molecule details ›
Chain: Bt
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: Bu
Molecule details ›
Chain: Bu
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: Bv
Molecule details ›
Chain: Bv
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: Bw
Molecule details ›
Chain: Bw
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: Bx
Molecule details ›
Chain: Bx
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: By
Molecule details ›
Chain: By
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: Bz
Molecule details ›
Chain: Bz
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
Peptide chain release factor 1, mitochondrial Chain: Aa
Molecule details ›
Chain: Aa
Length: 484 amino acids
Theoretical weight: 56.26 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75570 (Residues: 1-445; Coverage: 100%)
Gene name: MTRF1
Sequence domains:
E-site tRNA Chain: B7
Molecule details ›
Chain: B7
Length: 3 nucleotides
Theoretical weight: 895 Da
16S ribosomal RNA Chain: B8
Molecule details ›
Chain: B8
Length: 1561 nucleotides
Theoretical weight: 500.73 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
CP Val-tRNA(Val) Chain: B9
Molecule details ›
Chain: B9
Length: 72 nucleotides
Theoretical weight: 22.99 KDa
P-site Met-tRNA(Met) Chain: AG
Molecule details ›
Chain: AG
Length: 71 nucleotides
Theoretical weight: 22.69 KDa

Ligands and Environments

6 bound ligands:
Ligand K 34 x K
Ligand MG 228 x MG
Ligand VAL 1 x VAL
Ligand ZN 2 x ZN
Ligand FS2 1 x FS2
Ligand MET 1 x MET
8 modified residues:
Ligand 1MA 2 x 1MA
Ligand OMG 2 x OMG
Ligand OMU 1 x OMU
Ligand PSU 5 x PSU
Ligand 2MG 1 x 2MG
Ligand AYA 2 x AYA
Ligand SAC 1 x SAC
Ligand RSQ 1 x RSQ

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-16899
Expression system: Homo sapiens

Quick links

Citations

2 review citations

Decoding the Enigma: Translation Termination in Human Mitochondria.
Krüger et al. (2024)
1 more