7PNK | pdb_00007pnk

Unstacked compact Dunaliella PSII


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of Dunaliella Photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes.

Caspy, I.Fadeeva, M.Mazor, Y.Nelson, N.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.81150
  • Primary Citation Related Structures: 
    7PI0, 7PI5, 7PIN, 7PIW, 7PNK

  • PubMed Abstract: 

    Photosystem II (PSII) generates an oxidant whose redox potential is high enough to enable water oxidation , a substrate so abundant that it assures a practically unlimited electron source for life on earth . Our knowledge on the mechanism of water photooxidation was greatly advanced by high-resolution structures of prokaryotic PSII . Here, we show high-resolution cryogenic electron microscopy (cryo-EM) structures of eukaryotic PSII from the green alga Dunaliella salina at two distinct conformations. The conformers are also present in stacked PSII, exhibiting flexibility that may be relevant to the grana formation in chloroplasts of the green lineage. CP29, one of PSII associated light-harvesting antennae, plays a major role in distinguishing the two conformations of the supercomplex. We also show that the stacked PSII dimer, a form suggested to support the organisation of thylakoid membranes , can appear in many different orientations providing a flexible stacking mechanism for the arrangement of grana stacks in thylakoids. Our findings provide a structural basis for the heterogenous nature of the eukaryotic PSII on multiple levels.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Macromolecule Content 

  • Total Structure Weight: 865.68 kDa 
  • Atom Count: 60,673 
  • Modeled Residue Count: 6,142 
  • Deposited Residue Count: 6,142 
  • Unique protein chains: 24

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
Y [auth a]
336Dunaliella salinaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for D0FY08 (Dunaliella salina)
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UniProt GroupD0FY08
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
Z [auth b]
484Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRM6 (Dunaliella salina)
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UniProt GroupA0A1C8XRM6
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12AA [auth v],
C [auth V]
32Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY13 (Dunaliella salina)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinBA [auth c],
D [auth C]
449Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXY3 (Dunaliella salina)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinCA [auth d],
E [auth D]
348Dunaliella salinaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRK9 (Dunaliella salina)
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UniProt GroupA0A1C8XRK9
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaDA [auth e],
F [auth E]
76Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY01 (Dunaliella salina)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaEA [auth f],
G [auth F]
31Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRP4 (Dunaliella salina)
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UniProt GroupA0A1C8XRP4
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HFA [auth h],
H
67Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRP3 (Dunaliella salina)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IGA [auth i],
I
35Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXX5 (Dunaliella salina)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JHA [auth j],
J
36Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRM8 (Dunaliella salina)
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UniProt GroupA0A1C8XRM8
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KIA [auth k],
K
37Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXX2 (Dunaliella salina)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJA [auth l],
L
38Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY19 (Dunaliella salina)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MKA [auth m],
M
31Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ3 (Dunaliella salina)
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UniProt GroupD0FXZ3
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbOLA [auth o],
N [auth O]
238Dunaliella salinaMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbPMA [auth p],
O [auth P]
187Dunaliella salinaMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TNA [auth t],
P [auth T]
30Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY04 (Dunaliella salina)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbWOA [auth w],
Q [auth W]
44Dunaliella salinaMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbXPA [auth x],
R [auth X]
30Dunaliella salinaMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZQA [auth z],
S [auth Z]
61Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ2 (Dunaliella salina)
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein of LHCII type I, chloroplasticT [auth N]222Dunaliella salinaMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticU [auth G]221Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for A1XKU7 (Dunaliella salina)
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
CP26V [auth S]243Dunaliella salinaMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
LHCII M1W [auth Y]222Dunaliella salinaMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbURA [auth u],
X [auth U]
27Dunaliella salinaMutation(s): 0 

Small Molecules

Ligands 27 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
BC [auth B]
GJ [auth c]
HJ [auth c]
IJ [auth c]
LI [auth b]
BC [auth B],
GJ [auth c],
HJ [auth c],
IJ [auth c],
LI [auth b],
WC [auth C],
XC [auth C],
YC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



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AF [auth G]
DE [auth N]
EE [auth N]
FE [auth N]
GE [auth N]
AF [auth G],
DE [auth N],
EE [auth N],
FE [auth N],
GE [auth N],
GG [auth Y],
HE [auth N],
KG [auth Y],
LF [auth S],
LG [auth Y],
MG [auth Y],
OG [auth Y],
QF [auth S],
RF [auth S],
SE [auth G],
SF [auth S],
WE [auth G],
XE [auth G],
YE [auth G],
ZD [auth N],
ZE [auth G]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



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AE [auth N]
AI [auth b]
AJ [auth c]
BB [auth A]
BE [auth N]
AE [auth N],
AI [auth b],
AJ [auth c],
BB [auth A],
BE [auth N],
BF [auth G],
BI [auth b],
BJ [auth c],
CE [auth N],
CF [auth G],
CI [auth b],
DF [auth G],
DI [auth b],
EF [auth G],
EI [auth b],
FC [auth C],
FF [auth G],
FI [auth b],
GB [auth B],
GC [auth C],
GD [auth D],
GH [auth a],
HB [auth B],
HC [auth C],
HD [auth D],
HG [auth Y],
HH [auth a],
IB [auth B],
IC [auth C],
IE [auth N],
IG [auth Y],
IH [auth a],
JB [auth B],
JC [auth C],
JE [auth N],
JG [auth Y],
KB [auth B],
KC [auth C],
KE [auth N],
LB [auth B],
LC [auth C],
LE [auth N],
LH [auth a],
MB [auth B],
MC [auth C],
ME [auth N],
MF [auth S],
NB [auth B],
NC [auth C],
NF [auth S],
NG [auth Y],
OB [auth B],
OC [auth C],
OF [auth S],
PB [auth B],
PC [auth C],
PF [auth S],
PG [auth Y],
PI [auth c],
QB [auth B],
QC [auth C],
QG [auth Y],
QH [auth b],
QI [auth c],
QJ [auth d],
RB [auth B],
RC [auth C],
RG [auth Y],
RH [auth b],
RI [auth c],
RJ [auth d],
SB [auth B],
SG [auth Y],
SH [auth b],
SI [auth c],
TB [auth B],
TE [auth G],
TF [auth S],
TG [auth Y],
TH [auth b],
TI [auth c],
UB [auth B],
UE [auth G],
UF [auth S],
UH [auth b],
UI [auth c],
VB [auth B],
VE [auth G],
VF [auth S],
VH [auth b],
VI [auth c],
WA [auth A],
WF [auth S],
WH [auth b],
WI [auth c],
XA [auth A],
XF [auth S],
XH [auth b],
XI [auth c],
YA [auth A],
YF [auth S],
YH [auth b],
YI [auth c],
ZF [auth S],
ZH [auth b],
ZI [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



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AB [auth A],
JH [auth a],
KH [auth a],
ZA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
4RF

Query on 4RF



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BK [auth i],
DK [auth k],
SD [auth I],
UD [auth K]
Tripalmitoylglycerol
C51 H98 O6
PVNIQBQSYATKKL-UHFFFAOYSA-N
SQD

Query on SQD



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DB [auth A]
DD [auth C]
EC [auth B]
FK [auth m]
JI [auth b]
DB [auth A],
DD [auth C],
EC [auth B],
FK [auth m],
JI [auth b],
NH [auth a],
NJ [auth c],
OI [auth b],
WD [auth M],
ZB [auth B]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG

Query on LMG



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AC [auth B]
AD [auth C]
AK [auth h]
EB [auth A]
HK [auth w]
AC [auth B],
AD [auth C],
AK [auth h],
EB [auth A],
HK [auth w],
JJ [auth c],
KI [auth b],
KJ [auth c],
ND [auth D],
OH [auth a],
QD [auth H],
XJ [auth d],
YD [auth W],
ZC [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LMK

Query on LMK



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ED [auth C],
OJ [auth c]
trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium
C46 H94 N O7
BUXLRCGOLVGJEI-LHQLQFMZSA-O
PL9

Query on PL9



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JD [auth D],
TJ [auth d]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
PTY

Query on PTY



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AH [auth Y],
BH [auth Y]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG

Query on LHG



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CD [auth C]
DG [auth S]
EK [auth l]
KD [auth D]
KF [auth G]
CD [auth C],
DG [auth S],
EK [auth l],
KD [auth D],
KF [auth G],
LD [auth D],
MD [auth D],
MJ [auth c],
RE [auth N],
UJ [auth d],
VD [auth L],
VJ [auth d],
WJ [auth d],
YG [auth Y]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH

Query on 3PH



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CC [auth B],
FG [auth S],
GK [auth t],
MI [auth b],
XD [auth T]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA

Query on DGA



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BD [auth C]
CK [auth j]
DC [auth B]
LJ [auth c]
NI [auth b]
BD [auth C],
CK [auth j],
DC [auth B],
LJ [auth c],
NI [auth b],
TD [auth J]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEM

Query on HEM



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OD [auth F],
YJ [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NEX

Query on NEX



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CG [auth S],
JF [auth G],
QE [auth N],
XG [auth Y]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
XAT

Query on XAT



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IF [auth G],
PE [auth N],
WG [auth Y]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT

Query on LUT



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AG [auth S]
BG [auth S]
GF [auth G]
HF [auth G]
NE [auth N]
AG [auth S],
BG [auth S],
GF [auth G],
HF [auth G],
NE [auth N],
OE [auth N],
UG [auth Y],
VG [auth Y]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
C7Z

Query on C7Z



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II [auth b],
YB [auth B]
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
C40 H56 O2
JKQXZKUSFCKOGQ-ANDPMPNWSA-N
RRX

Query on RRX



Download:Ideal Coordinates CCD File
PD [auth H],
ZJ [auth h]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
CB [auth A]
CJ [auth c]
DJ [auth c]
EJ [auth c]
FJ [auth c]
CB [auth A],
CJ [auth c],
DJ [auth c],
EJ [auth c],
FJ [auth c],
GI [auth b],
HI [auth b],
ID [auth D],
MH [auth a],
SC [auth C],
SJ [auth d],
TC [auth C],
UC [auth C],
VC [auth C],
WB [auth B],
XB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LPX

Query on LPX



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EG [auth S](2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
C21 H44 N O7 P
YVYMBNSKXOXSKW-FQEVSTJZSA-N
OEX

Query on OEX



Download:Ideal Coordinates CCD File
CH [auth a],
SA [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
SPH

Query on SPH



Download:Ideal Coordinates CCD File
FB [auth A],
PH [auth a],
ZG [auth Y]
SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
RD [auth I]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
FD [auth D],
PJ [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
DH [auth a],
TA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
EH [auth a],
FH [auth a],
UA [auth A],
VA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
B,
Z [auth b]
L-PEPTIDE LINKINGC3 H7 N O4 SCYS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17
Israel Science FoundationIsrael199/21

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary