8OIP

28S mammalian mitochondrial small ribosomal subunit with mtRF1 and P-site tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Molecular basis of translation termination at noncanonical stop codons in human mitochondria.

Saurer, M.Leibundgut, M.Nadimpalli, H.P.Scaiola, A.Schonhut, T.Lee, R.G.Siira, S.J.Rackham, O.Dreos, R.Lenarcic, T.Kummer, E.Gatfield, D.Filipovska, A.Ban, N.

(2023) Science 380: 531-536

  • DOI: https://doi.org/10.1126/science.adf9890
  • Primary Citation of Related Structures:  
    8OIN, 8OIP, 8OIQ, 8OIR, 8OIS, 8OIT

  • PubMed Abstract: 

    The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.


  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialA [auth BX]303Sus scrofaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
bL31mB [auth Bd]126Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrial isoform 1D [auth AB]366Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S24E [auth AC]167Sus scrofaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A interacting protein 1F [auth AD]199Sus scrofaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
bS6m,Mitochondrial ribosomal protein S6G [auth AE]376Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S7H [auth AF]242Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S10J [auth AH]200Sus scrofaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S12L [auth AJ]139Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S14M [auth AK]128Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialN [auth AL]259Sus scrofaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialO [auth AM]135Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mP [auth AN]130Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialQ [auth AO]258Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18CR [auth AP]143Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialS [auth AQ]87Sus scrofaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S22T [auth AR]382Sus scrofaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
mS23U [auth AS]190Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S25V [auth AT]173Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S26W [auth AU]205Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AY01 (Sus scrofa)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S27X [auth AV]395Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2R1I0 (Sus scrofa)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Mitoribosomal protein ms28, mrps28Y [auth AW]188Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Death associated protein 3Z [auth AX]410Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialAA [auth AY]381Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S33BA [auth AZ]148Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 1, mitochondrialCA [auth Aa]474Homo sapiensMutation(s): 0 
Gene Names: MTRF1
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PHAROS:  O75570
GTEx:  ENSG00000120662 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S2DA [auth Ab]289Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain containing 1EA [auth Ac]118Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrial isoform X2FA [auth Ad]430Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mS39GA [auth Ae]692Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
uS9mHA [auth Ag]397Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S11IA [auth Ai]196Sus scrofaMutation(s): 1 
UniProt
Find proteins for A0A286ZJJ6 (Sus scrofa)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S34JA [auth Aj]505Sus scrofaMutation(s): 0 
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Entity ID: 3
MoleculeChains LengthOrganismImage
12S rRNAC [auth AA]962Sus scrofa
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Entity ID: 9
MoleculeChains LengthOrganismImage
P-site Met-tRNA(fMet)I [auth AG]72Homo sapiens
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Entity ID: 11
MoleculeChains LengthOrganismImage
mRNAK [auth AI]9Homo sapiens
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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VF [auth AX]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GDP
Query on GDP

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XF [auth AX]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
FS2
Query on FS2

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TF [auth AP],
UF [auth AT]
FE-S-O HYBRID CLUSTER
Fe4 O3 S2
DEAINXNPDRNZAH-UHFFFAOYSA-N
SPM
Query on SPM

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ZE [auth AA]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD
Query on SPD

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AF [auth AA]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN

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SF [auth AO]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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BF [auth AA]
CF [auth AA]
DF [auth AA]
EF [auth AA]
FF [auth AA]
BF [auth AA],
CF [auth AA],
DF [auth AA],
EF [auth AA],
FF [auth AA],
GF [auth AA],
HF [auth AA],
IF [auth AA],
JF [auth AA],
KF [auth AA],
LF [auth AA]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth AA]
AC [auth AA]
AD [auth AA]
AE [auth AA]
BB [auth AA]
AB [auth AA],
AC [auth AA],
AD [auth AA],
AE [auth AA],
BB [auth AA],
BC [auth AA],
BD [auth AA],
BE [auth AA],
CB [auth AA],
CC [auth AA],
CD [auth AA],
CE [auth AA],
DB [auth AA],
DC [auth AA],
DD [auth AA],
DE [auth AA],
EB [auth AA],
EC [auth AA],
ED [auth AA],
EE [auth AA],
FB [auth AA],
FC [auth AA],
FD [auth AA],
FE [auth AA],
GB [auth AA],
GC [auth AA],
GD [auth AA],
GE [auth AA],
HB [auth AA],
HC [auth AA],
HD [auth AA],
HE [auth AA],
IB [auth AA],
IC [auth AA],
ID [auth AA],
IE [auth AA],
JB [auth AA],
JC [auth AA],
JD [auth AA],
JE [auth AA],
KA [auth AA],
KB [auth AA],
KC [auth AA],
KD [auth AA],
KE [auth AA],
LA [auth AA],
LB [auth AA],
LC [auth AA],
LD [auth AA],
LE [auth AA],
MA [auth AA],
MB [auth AA],
MC [auth AA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
NA [auth AA],
NB [auth AA],
NC [auth AA],
ND [auth AA],
NE [auth AA],
NF [auth AD],
OA [auth AA],
OB [auth AA],
OC [auth AA],
OD [auth AA],
OE [auth AA],
OF [auth AG],
PA [auth AA],
PB [auth AA],
PC [auth AA],
PD [auth AA],
PE [auth AA],
PF [auth AI],
QA [auth AA],
QB [auth AA],
QC [auth AA],
QD [auth AA],
QE [auth AA],
QF [auth AJ],
RA [auth AA],
RB [auth AA],
RC [auth AA],
RD [auth AA],
RE [auth AA],
RF [auth AJ],
SA [auth AA],
SB [auth AA],
SC [auth AA],
SD [auth AA],
SE [auth AA],
TA [auth AA],
TB [auth AA],
TC [auth AA],
TD [auth AA],
TE [auth AA],
UA [auth AA],
UB [auth AA],
UC [auth AA],
UD [auth AA],
UE [auth AA],
VA [auth AA],
VB [auth AA],
VC [auth AA],
VD [auth AA],
VE [auth AA],
WA [auth AA],
WB [auth AA],
WC [auth AA],
WD [auth AA],
WE [auth AA],
WF [auth AX],
XA [auth AA],
XB [auth AA],
XC [auth AA],
XD [auth AA],
XE [auth AA],
YA [auth AA],
YB [auth AA],
YC [auth AA],
YD [auth AA],
YE [auth AA],
YF [auth Ab],
ZA [auth AA],
ZB [auth AA],
ZC [auth AA],
ZD [auth AA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
I [auth AG]L-PEPTIDE LINKINGC6 H11 N O3 SMET
AYA
Query on AYA
S [auth AQ]L-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland179190
Swiss National Science FoundationSwitzerland182341
European Molecular Biology Organization (EMBO)European Union1074-2019

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations, Refinement description
  • Version 2.1: 2024-04-24
    Changes: Data collection, Structure summary