8OIS

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialA [auth BX]292Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P49406 (Homo sapiens)
Explore P49406 
Go to UniProtKB:  P49406
PHAROS:  P49406
GTEx:  ENSG00000115364 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49406
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialB [auth Bd]128Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z7F7 (Homo sapiens)
Explore Q7Z7F7 
Go to UniProtKB:  Q7Z7F7
PHAROS:  Q7Z7F7
GTEx:  ENSG00000162910 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z7F7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialD [auth AB]323Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82673 (Homo sapiens)
Explore P82673 
Go to UniProtKB:  P82673
PHAROS:  P82673
GTEx:  ENSG00000061794 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82673
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialE [auth AC]167Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EL2 (Homo sapiens)
Explore Q96EL2 
Go to UniProtKB:  Q96EL2
GTEx:  ENSG00000062582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EL2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinF [auth AD]199Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT8 (Homo sapiens)
Explore Q9NWT8 
Go to UniProtKB:  Q9NWT8
PHAROS:  Q9NWT8
GTEx:  ENSG00000175756 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWT8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialG [auth AE]125Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82932 (Homo sapiens)
Explore P82932 
Go to UniProtKB:  P82932
PHAROS:  P82932
GTEx:  ENSG00000243927 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82932
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialH [auth AF]242Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2R9 (Homo sapiens)
Explore Q9Y2R9 
Go to UniProtKB:  Q9Y2R9
PHAROS:  Q9Y2R9
GTEx:  ENSG00000125445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2R9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialJ [auth AH]201Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82664 (Homo sapiens)
Explore P82664 
Go to UniProtKB:  P82664
PHAROS:  P82664
GTEx:  ENSG00000048544 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82664
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialL [auth AJ]138Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O15235 (Homo sapiens)
Explore O15235 
Go to UniProtKB:  O15235
PHAROS:  O15235
GTEx:  ENSG00000128626 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15235
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialM [auth AK]128Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60783 (Homo sapiens)
Explore O60783 
Go to UniProtKB:  O60783
PHAROS:  O60783
GTEx:  ENSG00000120333 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60783
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialN [auth AL]257Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82914 (Homo sapiens)
Explore P82914 
Go to UniProtKB:  P82914
PHAROS:  P82914
GTEx:  ENSG00000116898 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82914
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialO [auth AM]137Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D3 (Homo sapiens)
Explore Q9Y3D3 
Go to UniProtKB:  Q9Y3D3
PHAROS:  Q9Y3D3
GTEx:  ENSG00000182180 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3D3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialP [auth AN]130Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2R5 (Homo sapiens)
Explore Q9Y2R5 
Go to UniProtKB:  Q9Y2R5
PHAROS:  Q9Y2R5
GTEx:  ENSG00000239789 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2R5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialQ [auth AO]258Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y676 (Homo sapiens)
Explore Q9Y676 
Go to UniProtKB:  Q9Y676
PHAROS:  Q9Y676
GTEx:  ENSG00000204568 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y676
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialR [auth AP]142Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D5 (Homo sapiens)
Explore Q9Y3D5 
Go to UniProtKB:  Q9Y3D5
PHAROS:  Q9Y3D5
GTEx:  ENSG00000163319 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3D5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialS [auth AQ]87Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P82921 (Homo sapiens)
Explore P82921 
Go to UniProtKB:  P82921
PHAROS:  P82921
GTEx:  ENSG00000266472 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82921
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialT [auth AR]360Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82650 (Homo sapiens)
Explore P82650 
Go to UniProtKB:  P82650
PHAROS:  P82650
GTEx:  ENSG00000175110 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82650
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialU [auth AS]190Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D9 (Homo sapiens)
Explore Q9Y3D9 
Go to UniProtKB:  Q9Y3D9
PHAROS:  Q9Y3D9
GTEx:  ENSG00000181610 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3D9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialV [auth AT]173Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82663 (Homo sapiens)
Explore P82663 
Go to UniProtKB:  P82663
PHAROS:  P82663
GTEx:  ENSG00000131368 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82663
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialW [auth AU]205Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYN8 (Homo sapiens)
Explore Q9BYN8 
Go to UniProtKB:  Q9BYN8
GTEx:  ENSG00000125901 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYN8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialX [auth AV]414Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92552 (Homo sapiens)
Explore Q92552 
Go to UniProtKB:  Q92552
PHAROS:  Q92552
GTEx:  ENSG00000113048 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92552
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialY [auth AW]187Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Q9 (Homo sapiens)
Explore Q9Y2Q9 
Go to UniProtKB:  Q9Y2Q9
PHAROS:  Q9Y2Q9
GTEx:  ENSG00000147586 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2Q9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialZ [auth AX]398Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P51398 (Homo sapiens)
Explore P51398 
Go to UniProtKB:  P51398
PHAROS:  P51398
GTEx:  ENSG00000132676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51398
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialAA [auth AY]395Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92665 (Homo sapiens)
Explore Q92665 
Go to UniProtKB:  Q92665
PHAROS:  Q92665
GTEx:  ENSG00000102738 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92665
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialBA [auth AZ]106Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y291 (Homo sapiens)
Explore Q9Y291 
Go to UniProtKB:  Q9Y291
PHAROS:  Q9Y291
GTEx:  ENSG00000090263 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y291
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 1, mitochondrial,mtRF1(AAQ)CA [auth Aa]484Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for O75570 (Homo sapiens)
Explore O75570 
Go to UniProtKB:  O75570
PHAROS:  O75570
GTEx:  ENSG00000120662 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75570
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialDA [auth Ab]296Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y399 (Homo sapiens)
Explore Q9Y399 
Go to UniProtKB:  Q9Y399
PHAROS:  Q9Y399
GTEx:  ENSG00000122140 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y399
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1EA [auth Ac]118Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BP2 (Homo sapiens)
Explore Q96BP2 
Go to UniProtKB:  Q96BP2
PHAROS:  Q96BP2
GTEx:  ENSG00000172586 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96BP2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialFA [auth Ad]430Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82675 (Homo sapiens)
Explore P82675 
Go to UniProtKB:  P82675
PHAROS:  P82675
GTEx:  ENSG00000144029 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82675
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialGA [auth Ae]689Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EY7 (Homo sapiens)
Explore Q96EY7 
Go to UniProtKB:  Q96EY7
PHAROS:  Q96EY7
GTEx:  ENSG00000132300 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialHA [auth Ag]396Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82933 (Homo sapiens)
Explore P82933 
Go to UniProtKB:  P82933
PHAROS:  P82933
GTEx:  ENSG00000135972 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82933
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialIA [auth Ai]194Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P82912 (Homo sapiens)
Explore P82912 
Go to UniProtKB:  P82912
PHAROS:  P82912
GTEx:  ENSG00000181991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82912
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialJA [auth Aj]218Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82930 (Homo sapiens)
Explore P82930 
Go to UniProtKB:  P82930
PHAROS:  P82930
GTEx:  ENSG00000074071 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82930
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
12S rRNAC [auth AA]955Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains LengthOrganismImage
P-site Met-tRNA(Met)I [auth AG]71Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains LengthOrganismImage
mRNAK [auth AI]33Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
XF [auth AX]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
ZF [auth AX]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
FS2
Query on FS2

Download Ideal Coordinates CCD File 
UF [auth AP],
VF [auth AT]
FE-S-O HYBRID CLUSTER
Fe4 O3 S2
DEAINXNPDRNZAH-UHFFFAOYSA-N
MET
Query on MET

Download Ideal Coordinates CCD File 
RF [auth AG]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
TF [auth AO]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
CG [auth Ae]
KA [auth AA]
LA [auth AA]
MA [auth AA]
NA [auth AA]
CG [auth Ae],
KA [auth AA],
LA [auth AA],
MA [auth AA],
NA [auth AA],
OA [auth AA],
PA [auth AA],
QA [auth AA],
RA [auth AA],
SA [auth AA],
TA [auth AA],
UA [auth AA],
VA [auth AA],
WA [auth AA],
XA [auth AA],
YA [auth AA],
ZA [auth AA]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth AA]
AC [auth AA]
AD [auth AA]
AE [auth AA]
AF [auth AA]
AB [auth AA],
AC [auth AA],
AD [auth AA],
AE [auth AA],
AF [auth AA],
AG [auth Ab],
BB [auth AA],
BC [auth AA],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth Ad],
CB [auth AA],
CC [auth AA],
CD [auth AA],
CE [auth AA],
CF [auth AA],
DB [auth AA],
DC [auth AA],
DD [auth AA],
DE [auth AA],
DF [auth AA],
EB [auth AA],
EC [auth AA],
ED [auth AA],
EE [auth AA],
EF [auth AA],
FB [auth AA],
FC [auth AA],
FD [auth AA],
FE [auth AA],
FF [auth AA],
GB [auth AA],
GC [auth AA],
GD [auth AA],
GE [auth AA],
GF [auth AA],
HB [auth AA],
HC [auth AA],
HD [auth AA],
HE [auth AA],
HF [auth AA],
IB [auth AA],
IC [auth AA],
ID [auth AA],
IE [auth AA],
IF [auth AA],
JB [auth AA],
JC [auth AA],
JD [auth AA],
JE [auth AA],
JF [auth AA],
KB [auth AA],
KC [auth AA],
KD [auth AA],
KE [auth AA],
KF [auth AA],
LB [auth AA],
LC [auth AA],
LD [auth AA],
LE [auth AA],
LF [auth AA],
MB [auth AA],
MC [auth AA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
NB [auth AA],
NC [auth AA],
ND [auth AA],
NE [auth AA],
NF [auth AA],
OB [auth AA],
OC [auth AA],
OD [auth AA],
OE [auth AA],
OF [auth AA],
PB [auth AA],
PC [auth AA],
PD [auth AA],
PE [auth AA],
PF [auth AA],
QB [auth AA],
QC [auth AA],
QD [auth AA],
QE [auth AA],
QF [auth AD],
RB [auth AA],
RC [auth AA],
RD [auth AA],
RE [auth AA],
SB [auth AA],
SC [auth AA],
SD [auth AA],
SE [auth AA],
SF [auth AG],
TB [auth AA],
TC [auth AA],
TD [auth AA],
TE [auth AA],
UB [auth AA],
UC [auth AA],
UD [auth AA],
UE [auth AA],
VB [auth AA],
VC [auth AA],
VD [auth AA],
VE [auth AA],
WB [auth AA],
WC [auth AA],
WD [auth AA],
WE [auth AA],
WF [auth AU],
XB [auth AA],
XC [auth AA],
XD [auth AA],
XE [auth AA],
YB [auth AA],
YC [auth AA],
YD [auth AA],
YE [auth AA],
YF [auth AX],
ZB [auth AA],
ZC [auth AA],
ZD [auth AA],
ZE [auth AA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AYA
Query on AYA
S [auth AQ]L-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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 FoundationSwitzerland182341
Swiss National Science FoundationSwitzerland179190
European Molecular Biology Organization (EMBO)European Union1074-2019

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    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