7W5Z

Cryo-EM structure of Tetrahymena thermophila mitochondrial complex IV, composite dimer model


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of Tetrahymena 's respiratory chain reveal the diversity of eukaryotic core metabolism.

Zhou, L.Maldonado, M.Padavannil, A.Guo, F.Letts, J.A.

(2022) Science 376: 831-839

  • DOI: https://doi.org/10.1126/science.abn7747
  • Primary Citation of Related Structures:  
    7TGH, 7W5Z

  • PubMed Abstract: 

    Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate Tetrahymena thermophila (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt complex I (Tt-CI) and Tt-CIII 2 (Tt-SC I+III 2 ) and a structure of Tt-CIV 2 . Tt-SC I+III 2 (~2.3 megadaltons) is a curved assembly with structural and functional symmetry breaking. Tt-CIV 2 is a ~2.7-megadalton dimer with more than 50 subunits per protomer, including mitochondrial carriers and a TIM8 3 -TIM13 3 -like domain. Our structural and functional study of the T. thermophila respiratory chain reveals divergence in key components of eukaryotic respiration, thereby expanding our understanding of core metabolism.


  • Organizational Affiliation

    Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptideA [auth U1],
GB [auth u1]
98Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeB [auth U2],
HB [auth u2]
3,634Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q22C06 (Tetrahymena thermophila (strain SB210))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptideC [auth U3],
IB [auth u3]
34Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptideD [auth U4],
JB [auth u4]
30Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinE [auth U5],
KB [auth u5]
172Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transporter Sec61 alpha subunitF [auth U6],
LB [auth u6]
478Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1G [auth C1],
MB [auth c1]
688Tetrahymena thermophilaMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2H [auth C2],
NB [auth c2]
604Tetrahymena thermophilaMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ymf68I [auth C3],
OB [auth c3]
594Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome C oxidase subunit Vb proteinJ [auth 5B],
PB [auth 5b]
637Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeK [auth 6A],
QB [auth 6a]
130Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6BL [auth 6B],
RB [auth 6b]
230Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B-likeM [auth 6L],
SB [auth 6l]
88Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeN [auth 6C],
TB [auth 6c]
103Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeO [auth 7A],
UB [auth 7a]
133Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7CP [auth 7C],
VB [auth 7c]
236Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for W7X287 (Tetrahymena thermophila (strain SB210))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
CTF/NF-I domain-containing proteinQ [auth 7L],
WB [auth 7l]
990Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for Q22CI1 (Tetrahymena thermophila (strain SB210))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Oxoglutarate/malate translocator protein, putativeR [auth M1],
XB [auth m1]
346Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A4VDV3 (Tetrahymena thermophila (strain SB210))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate/malate carrier proteinS [auth M2],
YB [auth m2]
318Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Carrier proteinT [auth M3],
ZB [auth m3]
330Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Tim10/DDP family zinc finger proteinAC [auth t1],
U [auth T1]
72Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase small TIM subunit 2BC [auth t2],
V [auth T2]
72Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase small TIM subunit 3CC [auth t3],
W [auth T3]
93Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase small TIM subunit 4DC [auth t4],
X [auth T4]
68Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase small TIM subunit 5EC [auth t5],
Y [auth T5]
81Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase small TIM subunit 6FC [auth t6],
Z [auth T6]
72Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome condensation regulator RCC1 repeat proteinAA [auth BP],
GC [auth bp]
380Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-binding zinc finger CDGSH type proteinBA [auth FS],
HC [auth fs]
188Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase acyl carrier-like subunitCA [auth AC],
IC [auth ac]
127Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ymf67DA [auth Y7],
JC [auth y7]
453Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ymf70EA [auth Y0],
KC [auth y0]
89Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ymf75FA [auth Y5],
LC [auth y5]
190Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeGA [auth A],
MC [auth a]
490Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Protein phosphatase 2C, putativeHA [auth B],
NC [auth b]
473Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic nucleotide-binding domain proteinIA [auth C],
LD [auth c]
1,471Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
SURF1-like proteinJA [auth D],
OC [auth d]
402Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
TraB family proteinKA [auth E],
PC [auth e]
385Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeLA [auth F],
QC [auth f]
348Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT7MA [auth G],
RC [auth g]
318Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
SURF1-like proteinNA [auth H],
SC [auth h]
318Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT9OA [auth I],
TC [auth i]
252Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT10PA [auth J],
UC [auth j]
234Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT11QA [auth K],
VC [auth k]
231Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT12RA [auth L],
WC [auth l]
222Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeSA [auth M],
XC [auth m]
220Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeTA [auth N],
YC [auth n]
210Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT15UA [auth O],
ZC [auth o]
193Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT16AD [auth p],
VA [auth P]
175Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for I7M8Y9 (Tetrahymena thermophila (strain SB210))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeBD [auth q],
WA [auth Q]
173Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q23D87 (Tetrahymena thermophila (strain SB210))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT18CD [auth r],
XA [auth R]
173Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for I7MKT6 (Tetrahymena thermophila (strain SB210))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT19DD [auth s],
YA [auth S]
170Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeED [auth t],
ZA [auth T]
158Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q23VY4 (Tetrahymena thermophila (strain SB210))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeAB [auth U],
FD [auth u]
154Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q22DP8 (Tetrahymena thermophila (strain SB210))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT22BB [auth V],
GD [auth v]
149Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for I7MFV5 (Tetrahymena thermophila (strain SB210))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeCB [auth W],
HD [auth w]
124Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeDB [auth X],
ID [auth x]
122Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q22W32 (Tetrahymena thermophila (strain SB210))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT25EB [auth Y],
JD [auth y]
105Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for I7M9E7 (Tetrahymena thermophila (strain SB210))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit TT26FB [auth Z],
KD [auth z]
90Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for I7LTF1 (Tetrahymena thermophila (strain SB210))
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AF [auth Y0]
AG [auth c1]
AI [auth t]
BE [auth 5B]
BF [auth Y5]
AF [auth Y0],
AG [auth c1],
AI [auth t],
BE [auth 5B],
BF [auth Y5],
BG [auth c1],
BI [auth u],
CE [auth 5B],
CH [auth m3],
CI [auth v],
DE [auth 5B],
DH [auth m3],
EE [auth 7A],
EF [auth A],
EH [auth m3],
FE [auth 7A],
FF [auth B],
GE [auth 7C],
GF [auth E],
HF [auth E],
HG [auth c3],
HH [auth y7],
IE [auth 7C],
IF [auth F],
IH [auth y0],
JF [auth J],
JH [auth y5],
KE [auth M1],
KG [auth 5b],
LE [auth M1],
LF [auth L],
LG [auth 5b],
ME [auth M1],
MG [auth 7a],
MH [auth a],
NG [auth 7a],
NH [auth b],
OE [auth M2],
OG [auth 7c],
OH [auth e],
PF [auth N],
PG [auth 7c],
PH [auth e],
QE [auth M2],
QF [auth T],
QH [auth f],
RD [auth C1],
RE [auth M2],
RF [auth T],
RG [auth m1],
RH [auth j],
SD [auth C1],
SF [auth U],
TF [auth V],
TG [auth m1],
TH [auth k],
UE [auth M3],
UG [auth m1],
UH [auth l],
VE [auth M3],
WE [auth M3],
WG [auth m2],
YD [auth C3],
YG [auth m2],
YH [auth n],
ZE [auth Y7],
ZG [auth m2],
ZH [auth t]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA (Subject of Investigation/LOI)
Query on HEA

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MD [auth C1],
ND [auth C1],
VF [auth c1],
WF [auth c1]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1
Query on PC1

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AH [auth m2]
BH [auth m2]
CF [auth A]
DF [auth A]
DI [auth v]
AH [auth m2],
BH [auth m2],
CF [auth A],
DF [auth A],
DI [auth v],
EG [auth c3],
FG [auth c3],
GG [auth c3],
HE [auth 7C],
IG [auth c3],
JE [auth 7C],
KF [auth J],
KH [auth a],
LH [auth a],
NE [auth M1],
NF [auth N],
OF [auth N],
PE [auth M2],
QD [auth C1],
QG [auth 7c],
SE [auth M2],
SG [auth m1],
SH [auth j],
TE [auth M2],
UF [auth V],
VD [auth C3],
VG [auth m1],
WD [auth C3],
WH [auth n],
XD [auth C3],
XG [auth m2],
XH [auth n],
ZD [auth C3],
ZF [auth c1]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
FES (Subject of Investigation/LOI)
Query on FES

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FH [auth fs],
GH [auth fs],
XE [auth FS],
YE [auth FS]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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AE [auth 5B],
JG [auth 5b],
MF [auth M],
VH [auth m]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

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CG [auth c2]
DG [auth c2]
OD [auth C1]
TD [auth C2]
UD [auth C2]
CG [auth c2],
DG [auth c2],
OD [auth C1],
TD [auth C2],
UD [auth C2],
XF [auth c1]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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PD [auth C1],
YF [auth c1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
J [auth 5B],
PB [auth 5b]
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
J [auth 5B],
PB [auth 5b]
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
FME
Query on FME
M [auth 6L],
SB [auth 6l]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2.0
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM137929

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references
  • Version 1.2: 2022-06-01
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary