8OIQ

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
Mitochondrial ribosomal protein L12198Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mJ [auth BA]210Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TXR4 (Sus scrofa)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialK [auth BB]150Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480JJI1 (Sus scrofa)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL24mL [auth BC]216Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L27M [auth BD]148Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1U0F6 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L28N [auth BE]256Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZTW8 (Sus scrofa)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L47O [auth BF]250Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL30mP [auth BG]161Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1MIP3 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L32Q [auth BH]207Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
bL33mR [auth BI]65Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TLP9 (Sus scrofa)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L34S [auth BJ]95Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1UFR4 (Sus scrofa)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialT [auth BK]188Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2QZK0 (Sus scrofa)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L2U [auth BL]306Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287A143 (Sus scrofa)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ICT1V [auth BM]399Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A140UHW4 (Sus scrofa)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L4W [auth BN]294Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287B9C4 (Sus scrofa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L9X [auth BO]268Sus scrofaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L10Y [auth BP]257Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L11Z [auth BQ]192Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RU54 (Sus scrofa)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialAA [auth BR]197Sus scrofaMutation(s): 0 
UniProt
Find proteins for K7GP19 (Sus scrofa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L14BA [auth BS]325Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BMZ6 (Sus scrofa)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialCA [auth BT]296Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0HMG9 (Sus scrofa)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uL16mDA [auth BU]251Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RI89 (Sus scrofa)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
bL17mEA [auth BV]169Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18FA [auth BW]188Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VX01 (Sus scrofa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialGA [auth BX]303Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L20HA [auth BY]149Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZU56 (Sus scrofa)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L21IA [auth BZ]209Sus scrofaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L52, mitochondrialJA [auth Ba]160Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L53KA [auth Bb]112Sus scrofaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mL54LA [auth Bc]138Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
bL31mMA [auth Bd]126Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1ULI6 (Sus scrofa)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L57NA [auth Be]102Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
mL62 (ICT1)OA [auth Bf]205Sus scrofaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
mL64PA [auth Bg]222Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18AQA [auth Bh]196Sus scrofaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialRA [auth Bi]433Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L1, mitochondrialSA [auth Bj]304Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinTA [auth Bl]100Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L37UA [auth Bm]423Sus scrofaMutation(s): 0 
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Find proteins for A0A287BIV6 (Sus scrofa)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L38VA [auth Bn]380Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L39WA [auth Bo]334Sus scrofaMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L40XA [auth Bp]162Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L41YA [auth Bq]135Sus scrofaMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
mL42ZA [auth Br]142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrial isoform X2AB [auth Bs]159Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupF1S8U4
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
mL44BB [auth Bt]332Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L45CB [auth Bu]306Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L46DB [auth Bv]279Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SRT0 (Sus scrofa)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialEB [auth Bw]269Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480J9Z6 (Sus scrofa)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialFB [auth Bx]166Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287A0K2 (Sus scrofa)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L50GB [auth By]198Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3L9H6 (Sus scrofa)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L51HB [auth Bz]128Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1P1C8 (Sus scrofa)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 1, mitochondrialJB [auth Aa]474Homo sapiensMutation(s): 0 
Gene Names: MTRF1
UniProt & NIH Common Fund Data Resources
Find proteins for O75570 (Homo sapiens)
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PHAROS:  O75570
GTEx:  ENSG00000120662 
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Entity ID: 2
MoleculeChains LengthOrganismImage
E-site tRNAG [auth B7]3Sus scrofa
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Entity ID: 3
MoleculeChains LengthOrganismImage
16S rRNAH [auth B8]1,571Sus scrofa
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Entity ID: 4
MoleculeChains LengthOrganismImage
CP Phe-tRNAI [auth B9]73Sus scrofa
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Entity ID: 56
MoleculeChains LengthOrganismImage
P-site Met-tRNA(fMet)IB [auth AG]71Homo sapiens
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download Ideal Coordinates CCD File 
PK [auth AG]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
FES
Query on FES

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LK [auth Bh]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
PHE
Query on PHE

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VJ [auth B9]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
ZN
Query on ZN

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MK [auth Bl],
XJ [auth BH]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AJ [auth B8]
BJ [auth B8]
CJ [auth B8]
DJ [auth B8]
EJ [auth B8]
AJ [auth B8],
BJ [auth B8],
CJ [auth B8],
DJ [auth B8],
EJ [auth B8],
EK [auth BU],
FJ [auth B8],
GJ [auth B8],
HJ [auth B8],
IJ [auth B8],
IK [auth BW],
JJ [auth B8],
KJ [auth B8],
KK [auth Be],
LJ [auth B8],
MJ [auth B8],
NJ [auth B8],
OJ [auth B8],
PJ [auth B8],
QI [auth B8],
RI [auth B8],
SI [auth B8],
TI [auth B8],
UI [auth B8],
VI [auth B8],
WI [auth B8],
XI [auth B8],
YI [auth B8],
YJ [auth BL],
ZI [auth B8]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth B8]
AD [auth B8]
AE [auth B8]
AF [auth B8]
AG [auth B8]
AC [auth B8],
AD [auth B8],
AE [auth B8],
AF [auth B8],
AG [auth B8],
AH [auth B8],
AI [auth B8],
AK [auth BL],
BC [auth B8],
BD [auth B8],
BE [auth B8],
BF [auth B8],
BG [auth B8],
BH [auth B8],
BI [auth B8],
BK [auth BM],
CC [auth B8],
CD [auth B8],
CE [auth B8],
CF [auth B8],
CG [auth B8],
CH [auth B8],
CI [auth B8],
CK [auth BM],
DC [auth B8],
DD [auth B8],
DE [auth B8],
DF [auth B8],
DG [auth B8],
DH [auth B8],
DI [auth B8],
DK [auth BT],
EC [auth B8],
ED [auth B8],
EE [auth B8],
EF [auth B8],
EG [auth B8],
EH [auth B8],
EI [auth B8],
FC [auth B8],
FD [auth B8],
FE [auth B8],
FF [auth B8],
FG [auth B8],
FH [auth B8],
FI [auth B8],
FK [auth BV],
GC [auth B8],
GD [auth B8],
GE [auth B8],
GF [auth B8],
GG [auth B8],
GH [auth B8],
GI [auth B8],
GK [auth BV],
HC [auth B8],
HD [auth B8],
HE [auth B8],
HF [auth B8],
HG [auth B8],
HH [auth B8],
HI [auth B8],
HK [auth BV],
IC [auth B8],
ID [auth B8],
IE [auth B8],
IF [auth B8],
IG [auth B8],
IH [auth B8],
II [auth B8],
JC [auth B8],
JD [auth B8],
JE [auth B8],
JF [auth B8],
JG [auth B8],
JH [auth B8],
JI [auth B8],
JK [auth Be],
KB [auth B8],
KC [auth B8],
KD [auth B8],
KE [auth B8],
KF [auth B8],
KG [auth B8],
KH [auth B8],
KI [auth B8],
LB [auth B8],
LC [auth B8],
LD [auth B8],
LE [auth B8],
LF [auth B8],
LG [auth B8],
LH [auth B8],
LI [auth B8],
MB [auth B8],
MC [auth B8],
MD [auth B8],
ME [auth B8],
MF [auth B8],
MG [auth B8],
MH [auth B8],
MI [auth B8],
NB [auth B8],
NC [auth B8],
ND [auth B8],
NE [auth B8],
NF [auth B8],
NG [auth B8],
NH [auth B8],
NI [auth B8],
NK [auth Bq],
OB [auth B8],
OC [auth B8],
OD [auth B8],
OE [auth B8],
OF [auth B8],
OG [auth B8],
OH [auth B8],
OI [auth B8],
OK [auth Bx],
PB [auth B8],
PC [auth B8],
PD [auth B8],
PE [auth B8],
PF [auth B8],
PG [auth B8],
PH [auth B8],
PI [auth B8],
QB [auth B8],
QC [auth B8],
QD [auth B8],
QE [auth B8],
QF [auth B8],
QG [auth B8],
QH [auth B8],
QJ [auth B8],
RB [auth B8],
RC [auth B8],
RD [auth B8],
RE [auth B8],
RF [auth B8],
RG [auth B8],
RH [auth B8],
RJ [auth B8],
SB [auth B8],
SC [auth B8],
SD [auth B8],
SE [auth B8],
SF [auth B8],
SG [auth B8],
SH [auth B8],
SJ [auth B8],
TB [auth B8],
TC [auth B8],
TD [auth B8],
TE [auth B8],
TF [auth B8],
TG [auth B8],
TH [auth B8],
TJ [auth B8],
UB [auth B8],
UC [auth B8],
UD [auth B8],
UE [auth B8],
UF [auth B8],
UG [auth B8],
UH [auth B8],
UJ [auth B8],
VB [auth B8],
VC [auth B8],
VD [auth B8],
VE [auth B8],
VF [auth B8],
VG [auth B8],
VH [auth B8],
WB [auth B8],
WC [auth B8],
WD [auth B8],
WE [auth B8],
WF [auth B8],
WG [auth B8],
WH [auth B8],
WJ [auth B9],
XB [auth B8],
XC [auth B8],
XD [auth B8],
XE [auth B8],
XF [auth B8],
XG [auth B8],
XH [auth B8],
YB [auth B8],
YC [auth B8],
YD [auth B8],
YE [auth B8],
YF [auth B8],
YG [auth B8],
YH [auth B8],
ZB [auth B8],
ZC [auth B8],
ZD [auth B8],
ZE [auth B8],
ZF [auth B8],
ZG [auth B8],
ZH [auth B8],
ZJ [auth BL]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
AYA
Query on AYA
K [auth BB]L-PEPTIDE LINKINGC5 H9 N O3ALA
SAC
Query on SAC
AA [auth BR]L-PEPTIDE LINKINGC5 H9 N O4SER
THC
Query on THC
AB [auth Bs]L-PEPTIDE LINKINGC6 H11 N O4THR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
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: 2023-06-14
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Refinement description