7PIN | pdb_00007pin

Stacked compact Dunaliella PSII

Experimental Data Snapshot

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

Starting Model: experimental
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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: 2,180.39 kDa 
  • Atom Count: 152,240 
  • Modeled Residue Count: 14,846 
  • Deposited Residue Count: 14,846 
  • Unique protein chains: 25

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
XB [auth a1],
YA [auth A1],
Z [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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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinAA [auth b],
B,
YB [auth b1],
ZA [auth B1]		484Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRM6 (Dunaliella salina)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12AB [auth V1],
BA [auth v],
C [auth V],
ZB [auth v1]		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 proteinAC [auth c1],
BB [auth C1],
CA [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 proteinBC [auth d1],
CB [auth D1],
DA [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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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaCC [auth e1],
DB [auth E1],
EA [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 betaDC [auth f1],
EB [auth F1],
FA [auth f],
G [auth F]		31Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRP4 (Dunaliella salina)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HEC [auth h1],
FB [auth H1],
GA [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 IFC [auth i1],
GB [auth I1],
HA [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
PsbJGC [auth j1],
HB [auth J1],
IA [auth j],
J		36Dunaliella salinaMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KHC [auth k1],
IB [auth K1],
JA [auth k],
K		37Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXX2 (Dunaliella salina)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJB [auth L1],
KA [auth l],
L		38Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY19 (Dunaliella salina)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbMIC [auth m1],
KB [auth M1],
LA [auth m],
M		31Dunaliella salinaMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbOJC [auth o1],
LB [auth O1],
MA [auth o],
N [auth O]		238Dunaliella salinaMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbPKC [auth p1],
MB [auth P1],
NA [auth p],
O [auth P]		187Dunaliella salinaMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TLC [auth t1],
NB [auth T1],
OA [auth t],
P [auth T]		30Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY04 (Dunaliella salina)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbWMC [auth w1],
OB [auth W1],
PA [auth w],
Q [auth W]		44Dunaliella salinaMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbXNC [auth x1],
PB [auth X1],
QA [auth x],
R [auth X]		30Dunaliella salinaMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZOC [auth z1],
QB [auth Z1],
RA [auth z],
S [auth Z]		61Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ2 (Dunaliella salina)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
LHCII M3PC [auth n1],
RB [auth N1],
SA [auth n],
T [auth N]		222Dunaliella salinaMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticQC [auth g1],
SB [auth G1],
TA [auth g],
U [auth G]		221Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for A1XKU7 (Dunaliella salina)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
CP29RC [auth r1],
TB [auth R1],
UA [auth r],
V [auth R]		196Dunaliella salinaMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
CP26SC [auth s1],
UB [auth S1],
VA [auth s],
W [auth S]		243Dunaliella salinaMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
LHCII M1TC [auth y1],
VB [auth Y1],
WA [auth y],
X [auth Y]		222Dunaliella salinaMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbUUC [auth u1],
WB [auth U1],
XA [auth u],
Y [auth U]		27Dunaliella salinaMutation(s): 0 

Small Molecules

Ligands 30 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
AF [auth C]
AM [auth c]
BF [auth C]
BM [auth c]
BZ [auth b1]
AF [auth C],
AM [auth c],
BF [auth C],
BM [auth c],
BZ [auth b1],
CF [auth C],
CS [auth B1],
EL [auth b],
FE [auth B],
WZ [auth c1],
XS [auth C1],
XZ [auth c1],
YS [auth C1],
YZ [auth c1],
ZL [auth c],
ZS [auth C1]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL


Download:Ideal Coordinates CCD File
AEA [auth y1]
AH [auth G]
AO [auth g]
AQ [auth y]
AU [auth N1]
AEA [auth y1],
AH [auth G],
AO [auth g],
AQ [auth y],
AU [auth N1],
AV [auth G1],
AW [auth S1],
AX [auth Y1],
BBA [auth n1],
BH [auth G],
BN [auth n],
BO [auth g],
BP [auth s],
BQ [auth y],
BV [auth G1],
BX [auth Y1],
CBA [auth n1],
CDA [auth s1],
CH [auth G],
CJ [auth Y],
CO [auth g],
CQ [auth y],
DBA [auth n1],
DDA [auth s1],
DG [auth N],
DH [auth G],
DI [auth S],
DJ [auth Y],
DX [auth Y1],
EBA [auth n1],
EDA [auth s1],
EH [auth G],
EJ [auth Y],
EQ [auth y],
EU [auth N1],
FBA [auth n1],
FN [auth n],
FU [auth N1],
FW [auth S1],
GJ [auth Y],
GN [auth n],
GP [auth s],
GU [auth N1],
GW [auth S1],
HG [auth N],
HN [auth n],
HP [auth s],
HU [auth N1],
HW [auth S1],
IG [auth N],
II [auth S],
IN [auth n],
IP [auth s],
IU [auth N1],
JG [auth N],
JI [auth S],
JN [auth n],
KG [auth N],
KI [auth S],
LG [auth N],
MCA [auth r1],
NCA [auth r1],
PV [auth R1],
QBA [auth g1],
QO [auth r],
QV [auth R1],
RO [auth r],
SDA [auth y1],
SH [auth R],
TH [auth R],
TU [auth G1],
UBA [auth g1],
UN [auth g],
VBA [auth g1],
VW [auth Y1],
WBA [auth g1],
WDA [auth y1],
WG [auth G],
WP [auth y],
XAA [auth n1],
XBA [auth g1],
XCA [auth s1],
XDA [auth y1],
XU [auth G1],
YBA [auth g1],
YDA [auth y1],
YI [auth Y],
YN [auth g],
YU [auth G1],
ZN [auth g],
ZU [auth G1],
ZW [auth Y1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA


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ABA [auth n1]
ACA [auth g1]
AD [auth A]
ADA [auth s1]
AJ [auth Y]
ABA [auth n1],
ACA [auth g1],
AD [auth A],
ADA [auth s1],
AJ [auth Y],
AK [auth a],
AY [auth a1],
BCA [auth g1],
BD [auth A],
BDA [auth s1],
BEA [auth y1],
BJ [auth Y],
BR [auth A1],
BU [auth N1],
BW [auth S1],
CCA [auth g1],
CEA [auth y1],
CN [auth n],
CP [auth s],
CU [auth N1],
CV [auth G1],
CW [auth S1],
CX [auth Y1],
DCA [auth g1],
DEA [auth y1],
DK [auth a],
DN [auth n],
DO [auth g],
DP [auth s],
DQ [auth y],
DU [auth N1],
DV [auth G1],
DW [auth S1],
ED [auth A],
EEA [auth y1],
EG [auth N],
EI [auth S],
EN [auth n],
EO [auth g],
EP [auth s],
EV [auth G1],
EW [auth S1],
EX [auth Y1],
FDA [auth s1],
FEA [auth y1],
FG [auth N],
FH [auth G],
FI [auth S],
FJ [auth Y],
FO [auth g],
FP [auth s],
FQ [auth y],
FV [auth G1],
FX [auth Y1],
FZ [auth c1],
GAA [auth d1],
GBA [auth n1],
GDA [auth s1],
GG [auth N],
GH [auth G],
GI [auth S],
GO [auth g],
GQ [auth y],
GS [auth C1],
GV [auth G1],
GX [auth Y1],
GY [auth b1],
GZ [auth c1],
HAA [auth d1],
HBA [auth n1],
HDA [auth s1],
HH [auth G],
HI [auth S],
HJ [auth Y],
HO [auth g],
HQ [auth y],
HR [auth B1],
HS [auth C1],
HT [auth D1],
HX [auth Y1],
HY [auth b1],
HZ [auth c1],
IBA [auth n1],
IDA [auth s1],
IH [auth G],
IJ [auth Y],
IL [auth c],
IQ [auth y],
IR [auth B1],
IS [auth C1],
IT [auth D1],
IW [auth S1],
IX [auth Y1],
IY [auth b1],
IZ [auth c1],
JBA [auth n1],
JCA [auth r1],
JDA [auth s1],
JE [auth C],
JH [auth G],
JJ [auth Y],
JK [auth b],
JL [auth c],
JM [auth d],
JP [auth s],
JQ [auth y],
JR [auth B1],
JS [auth C1],
JU [auth N1],
JW [auth S1],
JY [auth b1],
JZ [auth c1],
KBA [auth n1],
KCA [auth r1],
KD [auth B],
KDA [auth s1],
KE [auth C],
KF [auth D],
KJ [auth Y],
KK [auth b],
KL [auth c],
KM [auth d],
KN [auth n],
KP [auth s],
KR [auth B1],
KS [auth C1],
KU [auth N1],
KW [auth S1],
KY [auth b1],
KZ [auth c1],
LCA [auth r1],
LD [auth B],
LDA [auth s1],
LE [auth C],
LF [auth D],
LI [auth S],
LJ [auth Y],
LK [auth b],
LL [auth c],
LN [auth n],
LP [auth s],
LR [auth B1],
LS [auth C1],
LU [auth N1],
LW [auth S1],
LY [auth b1],
LZ [auth c1],
MD [auth B],
ME [auth C],
MG [auth N],
MI [auth S],
MK [auth b],
ML [auth c],
MN [auth n],
MP [auth s],
MR [auth B1],
MS [auth C1],
MU [auth N1],
MV [auth R1],
MW [auth S1],
MY [auth b1],
MZ [auth c1],
ND [auth B],
NE [auth C],
NG [auth N],
NI [auth S],
NK [auth b],
NL [auth c],
NN [auth n],
NO [auth r],
NP [auth s],
NR [auth B1],
NS [auth C1],
NU [auth N1],
NV [auth R1],
NW [auth S1],
NY [auth b1],
NZ [auth c1],
OCA [auth r1],
OD [auth B],
OE [auth C],
OG [auth N],
OI [auth S],
OK [auth b],
OL [auth c],
ON [auth n],
OO [auth r],
OP [auth s],
OR [auth B1],
OS [auth C1],
OV [auth R1],
OW [auth S1],
OY [auth b1],
OZ [auth c1],
PCA [auth r1],
PD [auth B],
PE [auth C],
PG [auth N],
PH [auth R],
PI [auth S],
PK [auth b],
PL [auth c],
PO [auth r],
PP [auth s],
PR [auth B1],
PS [auth C1],
PY [auth b1],
PZ [auth c1],
QCA [auth r1],
QD [auth B],
QE [auth C],
QG [auth N],
QH [auth R],
QI [auth S],
QK [auth b],
QL [auth c],
QR [auth B1],
QS [auth C1],
QY [auth b1],
QZ [auth c1],
RBA [auth g1],
RCA [auth r1],
RD [auth B],
RE [auth C],
RH [auth R],
RI [auth S],
RK [auth b],
RL [auth c],
RR [auth B1],
RS [auth C1],
RV [auth R1],
RY [auth b1],
RZ [auth c1],
SBA [auth g1],
SD [auth B],
SE [auth C],
SK [auth b],
SL [auth c],
SO [auth r],
SR [auth B1],
SS [auth C1],
SV [auth R1],
SY [auth b1],
TBA [auth g1],
TD [auth B],
TDA [auth y1],
TE [auth C],
TK [auth b],
TL [auth c],
TO [auth r],
TR [auth B1],
TV [auth R1],
TY [auth b1],
UD [auth B],
UDA [auth y1],
UE [auth C],
UH [auth R],
UK [auth b],
UL [auth c],
UO [auth r],
UR [auth B1],
UU [auth G1],
UV [auth R1],
UY [auth b1],
VD [auth B],
VDA [auth y1],
VE [auth C],
VH [auth R],
VK [auth b],
VN [auth g],
VO [auth r],
VR [auth B1],
VU [auth G1],
VX [auth a1],
VY [auth b1],
WD [auth B],
WH [auth R],
WK [auth b],
WN [auth g],
WQ [auth A1],
WR [auth B1],
WU [auth G1],
WW [auth Y1],
WX [auth a1],
XD [auth B],
XG [auth G],
XH [auth R],
XK [auth b],
XN [auth g],
XP [auth y],
XQ [auth A1],
XW [auth Y1],
XX [auth a1],
YAA [auth n1],
YCA [auth s1],
YD [auth B],
YG [auth G],
YJ [auth a],
YK [auth b],
YP [auth y],
YQ [auth A1],
YW [auth Y1],
ZAA [auth n1],
ZBA [auth g1],
ZC [auth A],
ZCA [auth s1],
ZD [auth B],
ZDA [auth y1],
ZG [auth G],
ZI [auth Y],
ZJ [auth a],
ZP [auth y]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO


Download:Ideal Coordinates CCD File
AR [auth A1]
BK [auth a]
CD [auth A]
CK [auth a]
DD [auth A]
AR [auth A1],
BK [auth a],
CD [auth A],
CK [auth a],
DD [auth A],
YX [auth a1],
ZQ [auth A1],
ZX [auth a1]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
4RF

Query on 4RF


Download:Ideal Coordinates CCD File
RAA [auth i1]
TAA [auth k1]
TT [auth I1]
UM [auth i]
VT [auth K1]
RAA [auth i1],
TAA [auth k1],
TT [auth I1],
UM [auth i],
VT [auth K1],
WF [auth I],
WM [auth k],
YF [auth K]
Tripalmitoylglycerol
C51 H98 O6
PVNIQBQSYATKKL-UHFFFAOYSA-N
SQD

Query on SQD


Download:Ideal Coordinates CCD File
AG [auth M]
AS [auth B1]
CL [auth b]
CY [auth a1]
DAA [auth c1]
AG [auth M],
AS [auth B1],
CL [auth b],
CY [auth a1],
DAA [auth c1],
DE [auth B],
DR [auth A1],
ET [auth C1],
EZ [auth b1],
FK [auth a],
FS [auth B1],
GD [auth A],
GM [auth c],
HF [auth C],
HL [auth b],
IE [auth B],
UAA [auth m1],
XT [auth M1],
YM [auth m],
ZY [auth b1]
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


Download:Ideal Coordinates CCD File
AAA [auth c1]
AN [auth w]
AT [auth C1]
AZ [auth b1]
BS [auth B1]
AAA [auth c1],
AN [auth w],
AT [auth C1],
AZ [auth b1],
BS [auth B1],
BT [auth C1],
CG [auth W],
CM [auth c],
DF [auth C],
DL [auth b],
DM [auth c],
DY [auth a1],
EE [auth B],
EF [auth C],
ER [auth A1],
GK [auth a],
HD [auth A],
NAA [auth d1],
OT [auth D1],
QAA [auth h1],
QM [auth d],
RF [auth D],
RT [auth H1],
TM [auth h],
UF [auth H],
WAA [auth w1],
ZT [auth W1],
ZZ [auth c1]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LMK

Query on LMK


Download:Ideal Coordinates CCD File
EAA [auth c1],
FT [auth C1],
HM [auth c],
IF [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


Download:Ideal Coordinates CCD File
JAA [auth d1],
KT [auth D1],
MM [auth d],
NF [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


Download:Ideal Coordinates CCD File
MEA [auth y1]
NEA [auth y1]
PX [auth Y1]
QQ [auth y]
QX [auth Y1]
MEA [auth y1],
NEA [auth y1],
PX [auth Y1],
QQ [auth y],
QX [auth Y1],
RQ [auth y],
SJ [auth Y],
TJ [auth Y]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG

Query on LHG


Download:Ideal Coordinates CCD File
CAA [auth c1]
DT [auth C1]
FM [auth c]
GF [auth C]
ICA [auth g1]
CAA [auth c1],
DT [auth C1],
FM [auth c],
GF [auth C],
ICA [auth g1],
KAA [auth d1],
KEA [auth y1],
LAA [auth d1],
LT [auth D1],
LV [auth G1],
MAA [auth d1],
MO [auth g],
MT [auth D1],
NM [auth d],
NT [auth D1],
NX [auth Y1],
OF [auth D],
OH [auth G],
OM [auth d],
OQ [auth y],
PBA [auth n1],
PDA [auth s1],
PF [auth D],
PM [auth d],
QF [auth D],
QJ [auth Y],
SU [auth N1],
SW [auth S1],
TN [auth n],
TP [auth s],
VG [auth N],
VI [auth S],
WT [auth L1],
XM [auth l],
ZF [auth L]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH

Query on 3PH


Download:Ideal Coordinates CCD File
BG [auth T]
CZ [auth b1]
DS [auth B1]
FL [auth b]
GE [auth B]
BG [auth T],
CZ [auth b1],
DS [auth B1],
FL [auth b],
GE [auth B],
RDA [auth s1],
UW [auth S1],
VAA [auth t1],
VP [auth s],
XI [auth S],
YT [auth T1],
ZM [auth t]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA

Query on DGA


Download:Ideal Coordinates CCD File
BAA [auth c1]
CT [auth C1]
DZ [auth b1]
EM [auth c]
ES [auth B1]
BAA [auth c1],
CT [auth C1],
DZ [auth b1],
EM [auth c],
ES [auth B1],
FF [auth C],
GL [auth b],
HE [auth B],
SAA [auth j1],
UT [auth J1],
VM [auth j],
XF [auth J]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEM

Query on HEM


Download:Ideal Coordinates CCD File
OAA [auth f1],
PT [auth F1],
RM [auth f],
SF [auth F]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NEX

Query on NEX


Download:Ideal Coordinates CCD File
AI [auth R]
HCA [auth g1]
JEA [auth y1]
KV [auth G1]
LO [auth g]
AI [auth R],
HCA [auth g1],
JEA [auth y1],
KV [auth G1],
LO [auth g],
MX [auth Y1],
NH [auth G],
NQ [auth y],
OBA [auth n1],
ODA [auth s1],
PJ [auth Y],
RU [auth N1],
RW [auth S1],
SN [auth n],
SP [auth s],
UCA [auth r1],
UG [auth N],
UI [auth S],
XV [auth R1],
YO [auth r]
(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


Download:Ideal Coordinates CCD File
GCA [auth g1]
IEA [auth y1]
JV [auth G1]
KO [auth g]
LX [auth Y1]
GCA [auth g1],
IEA [auth y1],
JV [auth G1],
KO [auth g],
LX [auth Y1],
MH [auth G],
MQ [auth y],
NBA [auth n1],
OJ [auth Y],
QU [auth N1],
RN [auth n],
TCA [auth r1],
TG [auth N],
WV [auth R1],
XO [auth r],
ZH [auth R]
(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


Download:Ideal Coordinates CCD File
ECA [auth g1]
FCA [auth g1]
GEA [auth y1]
HEA [auth y1]
HV [auth G1]
ECA [auth g1],
FCA [auth g1],
GEA [auth y1],
HEA [auth y1],
HV [auth G1],
IO [auth g],
IV [auth G1],
JO [auth g],
JX [auth Y1],
KH [auth G],
KQ [auth y],
KX [auth Y1],
LBA [auth n1],
LH [auth G],
LQ [auth y],
MBA [auth n1],
MDA [auth s1],
MJ [auth Y],
NDA [auth s1],
NJ [auth Y],
OU [auth N1],
PN [auth n],
PU [auth N1],
PW [auth S1],
QN [auth n],
QP [auth s],
QW [auth S1],
RG [auth N],
RP [auth s],
SCA [auth r1],
SG [auth N],
SI [auth S],
TI [auth S],
VV [auth R1],
WO [auth r],
YH [auth R]
(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


Download:Ideal Coordinates CCD File
BL [auth b],
CE [auth B],
YY [auth b1],
ZR [auth B1]		(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
PAA [auth h1],
QT [auth H1],
SM [auth h],
TF [auth H]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR


Download:Ideal Coordinates CCD File
AE [auth B]
AL [auth b]
BE [auth B]
BY [auth a1]
CR [auth A1]
AE [auth B],
AL [auth b],
BE [auth B],
BY [auth a1],
CR [auth A1],
EK [auth a],
FD [auth A],
IAA [auth d1],
JT [auth D1],
LM [auth d],
MF [auth D],
SZ [auth c1],
TS [auth C1],
TZ [auth c1],
US [auth C1],
UZ [auth c1],
VL [auth c],
VS [auth C1],
VZ [auth c1],
WE [auth C],
WL [auth c],
WS [auth C1],
WY [auth b1],
XE [auth C],
XL [auth c],
XR [auth B1],
XY [auth b1],
YE [auth C],
YL [auth c],
YR [auth B1],
ZE [auth C],
ZK [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT


Download:Ideal Coordinates CCD File
BI [auth R],
VCA [auth r1],
YV [auth R1],
ZO [auth r]		DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LPX

Query on LPX


Download:Ideal Coordinates CCD File
QDA [auth s1],
TW [auth S1],
UP [auth s],
WI [auth S]		(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
C21 H44 N O7 P
YVYMBNSKXOXSKW-FQEVSTJZSA-N
ERG

Query on ERG


Download:Ideal Coordinates CCD File
AP [auth r],
CI [auth R],
WCA [auth r1],
ZV [auth R1]		ERGOSTEROL
C28 H44 O
DNVPQKQSNYMLRS-APGDWVJJSA-N
OEX

Query on OEX


Download:Ideal Coordinates CCD File
RX [auth a1],
SQ [auth A1],
UJ [auth a],
VC [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
SPH

Query on SPH


Download:Ideal Coordinates CCD File
EY [auth a1]
FR [auth A1]
HK [auth a]
ID [auth A]
LEA [auth y1]
EY [auth a1],
FR [auth A1],
HK [auth a],
ID [auth A],
LEA [auth y1],
OX [auth Y1],
PQ [auth y],
RJ [auth Y]
SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
ST [auth I1],
VF [auth I]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT

Query on BCT


Download:Ideal Coordinates CCD File
FAA [auth d1],
GT [auth D1],
IM [auth d],
JF [auth D]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


Download:Ideal Coordinates CCD File
SX [auth a1],
TQ [auth A1],
VJ [auth a],
WC [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
TX [auth a1]
UQ [auth A1]
UX [auth a1]
VQ [auth A1]
WJ [auth a]
TX [auth a1],
UQ [auth A1],
UX [auth a1],
VQ [auth A1],
WJ [auth a],
XC [auth A],
XJ [auth a],
YC [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA


Download:Ideal Coordinates CCD File
FY [auth a1],
GR [auth A1],
IK [auth a],
JD [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP		RC [auth r1],
TB [auth R1],
UA [auth r],
V [auth R]		L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



View more in-depth experimental data

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: 2024-10-23
    Changes: Data collection, Refinement description, Structure summary