7PIW | pdb_00007piw

Stacked stretched Dunaliella PSII


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7PIW

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: 2,170.3 kDa 
  • Atom Count: 151,508 
  • Modeled Residue Count: 14,859 
  • Deposited Residue Count: 14,872 
  • Unique protein chains: 27

Macromolecules

Find similar proteins by:|  3D Structure
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)
Explore D0FY08 
Go to UniProtKB:  D0FY08
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FY08
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinAA [auth b],
B,
YB [auth b1],
ZA [auth B1]
484Dunaliella salinaMutation(s): 2 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY05 (Dunaliella salina)
Explore D0FY05 
Go to UniProtKB:  D0FY05
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FY05
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore D0FY13 
Go to UniProtKB:  D0FY13
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FY13
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore D0FXY3 
Go to UniProtKB:  D0FXY3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXY3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinBC [auth d1],
CB [auth D1],
DA [auth d],
E [auth D]
348Dunaliella salinaMutation(s): 1 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for D0FXW8 (Dunaliella salina)
Explore D0FXW8 
Go to UniProtKB:  D0FXW8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXW8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore D0FY01 
Go to UniProtKB:  D0FY01
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FY01
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 D0FY18 (Dunaliella salina)
Explore D0FY18 
Go to UniProtKB:  D0FY18
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FY18
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HEC [auth h1],
FB [auth H1],
GA [auth h],
H
67Dunaliella salinaMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY02 (Dunaliella salina)
Explore D0FY02 
Go to UniProtKB:  D0FY02
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FY02
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore D0FXX5 
Go to UniProtKB:  D0FXX5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXX5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JGC [auth j1],
HB [auth J1],
IA [auth j],
J
36Dunaliella salinaMutation(s): 3 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXW2 (Dunaliella salina)
Explore D0FXW2 
Go to UniProtKB:  D0FXW2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXW2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore D0FXX2 
Go to UniProtKB:  D0FXX2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXX2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore D0FY19 
Go to UniProtKB:  D0FY19
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FY19
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MLA [auth m],
M
32Dunaliella salinaMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ3 (Dunaliella salina)
Explore D0FXZ3 
Go to UniProtKB:  D0FXZ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXZ3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbOJC [auth o1],
LB [auth O1],
MA [auth o],
N [auth O]
238Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbPKC [auth p1],
MB [auth P1],
NA [auth p],
O [auth P]
187Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
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)
Explore D0FY04 
Go to UniProtKB:  D0FY04
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FY04
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbWMC [auth w1],
OB [auth W1],
PA [auth w],
Q [auth W]
44Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbXNC [auth x1],
PB [auth X1],
QA [auth x],
R [auth X]
30Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbZOC [auth z1],
QB [auth Z1],
RA [auth z],
S [auth Z]
61Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
LHCII M3PC [auth n1],
RB [auth N1],
SA [auth n],
T [auth N]
222Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
LHCII M2QC [auth g1],
SB [auth G1],
TA [auth g],
U [auth G]
221Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
CP29UA [auth r],
V [auth R]
202Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
CP26SC [auth s1],
UB [auth S1],
VA [auth s],
W [auth S]
243Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
LHCII M1TC [auth y1],
VB [auth Y1],
WA [auth y],
X [auth Y]
222Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbUUC [auth u1],
WB [auth U1],
XA [auth u],
Y [auth U]
27Dunaliella salinaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MIC [auth m1],
KB [auth M1]
31Dunaliella salinaMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ3 (Dunaliella salina)
Explore D0FXZ3 
Go to UniProtKB:  D0FXZ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXZ3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
CP29RC [auth r1],
TB [auth R1]
202Dunaliella salinaMutation(s): 0 

Small Molecules

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

Query on DGD



Download:Ideal Coordinates CCD File
BF [auth C]
EZ [auth c1]
FS [auth C1]
FZ [auth c1]
GS [auth C1]
BF [auth C],
EZ [auth c1],
FS [auth C1],
FZ [auth c1],
GS [auth C1],
GZ [auth c1],
HS [auth C1],
JY [auth b1],
KR [auth B1],
ML [auth c],
NL [auth c],
OL [auth c],
QL [auth c],
XE [auth C],
YE [auth C],
ZE [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



Download:Ideal Coordinates CCD File
ADA [auth y1]
AG [auth N]
AI [auth S]
BG [auth N]
BI [auth S]
ADA [auth y1],
AG [auth N],
AI [auth S],
BG [auth N],
BI [auth S],
BU [auth G1],
CBA [auth g1],
CG [auth N],
CO [auth r],
DBA [auth g1],
DN [auth g],
DO [auth r],
DW [auth Y1],
EBA [auth g1],
EDA [auth y1],
FAA [auth n1],
FBA [auth g1],
FCA [auth s1],
FDA [auth y1],
FP [auth y],
FU [auth G1],
GBA [auth g1],
GDA [auth y1],
GU [auth G1],
HN [auth g],
HU [auth G1],
HW [auth Y1],
IDA [auth y1],
IN [auth g],
IT [auth N1],
IU [auth G1],
IV [auth S1],
IW [auth Y1],
JAA [auth n1],
JH [auth R],
JN [auth g],
JP [auth y],
JU [auth G1],
JW [auth Y1],
KAA [auth n1],
KCA [auth s1],
KH [auth R],
KM [auth n],
KN [auth g],
KO [auth s],
KP [auth y],
LAA [auth n1],
LCA [auth s1],
LN [auth g],
LP [auth y],
LW [auth Y1],
MAA [auth n1],
MCA [auth s1],
MT [auth N1],
NAA [auth n1],
NG [auth G],
NP [auth y],
NT [auth N1],
NV [auth S1],
OM [auth n],
OT [auth N1],
OV [auth S1],
PI [auth Y],
PM [auth n],
PO [auth s],
PT [auth N1],
PV [auth S1],
QM [auth n],
QO [auth s],
QT [auth N1],
RG [auth G],
RM [auth n],
RO [auth s],
SG [auth G],
SM [auth n],
TG [auth G],
TI [auth Y],
UBA [auth r1],
UF [auth N],
UG [auth G],
UH [auth S],
UI [auth Y],
VBA [auth r1],
VG [auth G],
VI [auth Y],
XI [auth Y],
XU [auth R1],
YAA [auth g1],
YF [auth N],
YU [auth R1],
ZF [auth N],
ZH [auth S]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



Download:Ideal Coordinates CCD File
ABA [auth g1]
AD [auth A]
AH [auth G]
AJ [auth Y]
AK [auth b]
ABA [auth g1],
AD [auth A],
AH [auth G],
AJ [auth Y],
AK [auth b],
AL [auth c],
AO [auth r],
AR [auth B1],
AS [auth C1],
AV [auth R1],
AY [auth b1],
BBA [auth g1],
BD [auth A],
BDA [auth y1],
BJ [auth Y],
BK [auth b],
BL [auth c],
BO [auth r],
BR [auth B1],
BV [auth R1],
BY [auth b1],
CDA [auth y1],
CI [auth S],
CJ [auth Y],
CK [auth b],
CL [auth c],
CR [auth B1],
CU [auth G1],
CV [auth R1],
CY [auth b1],
DDA [auth y1],
DG [auth N],
DI [auth S],
DK [auth b],
DL [auth c],
DR [auth B1],
DU [auth G1],
DX [auth a1],
DY [auth b1],
ED [auth A],
EG [auth N],
EI [auth S],
EK [auth b],
EL [auth c],
EN [auth g],
EO [auth r],
EQ [auth A1],
ER [auth B1],
EU [auth G1],
EW [auth Y1],
EX [auth a1],
FG [auth N],
FI [auth S],
FK [auth b],
FL [auth c],
FN [auth g],
FO [auth r],
FQ [auth A1],
FW [auth Y1],
FX [auth a1],
GAA [auth n1],
GCA [auth s1],
GE [auth C],
GG [auth N],
GH [auth R],
GI [auth S],
GK [auth b],
GL [auth c],
GN [auth g],
GO [auth r],
GP [auth y],
GQ [auth A1],
GW [auth Y1],
HAA [auth n1],
HBA [auth g1],
HCA [auth s1],
HDA [auth y1],
HE [auth C],
HF [auth D],
HG [auth N],
HH [auth R],
HI [auth S],
HK [auth b],
HL [auth c],
HO [auth r],
HP [auth y],
IAA [auth n1],
IBA [auth g1],
ICA [auth s1],
IE [auth C],
IF [auth D],
IH [auth R],
II [auth S],
IK [auth b],
IO [auth r],
IP [auth y],
IX [auth a1],
JBA [auth g1],
JCA [auth s1],
JD [auth B],
JDA [auth y1],
JE [auth C],
JK [auth b],
JO [auth r],
JQ [auth A1],
JT [auth N1],
JV [auth S1],
KBA [auth g1],
KD [auth B],
KDA [auth y1],
KE [auth C],
KK [auth b],
KT [auth N1],
KU [auth G1],
KV [auth S1],
KW [auth Y1],
LBA [auth g1],
LD [auth B],
LDA [auth y1],
LE [auth C],
LH [auth R],
LK [auth b],
LM [auth n],
LO [auth s],
LT [auth N1],
LU [auth G1],
LV [auth S1],
MD [auth B],
MDA [auth y1],
ME [auth C],
MH [auth R],
MK [auth b],
MM [auth n],
MN [auth g],
MO [auth s],
MP [auth y],
MU [auth G1],
MV [auth S1],
MW [auth Y1],
NCA [auth s1],
ND [auth B],
NDA [auth y1],
NE [auth C],
NH [auth R],
NJ [auth a],
NM [auth n],
NN [auth g],
NO [auth s],
NU [auth G1],
NW [auth Y1],
NY [auth c1],
OAA [auth n1],
OCA [auth s1],
OD [auth B],
OE [auth C],
OG [auth G],
OH [auth R],
OJ [auth a],
ON [auth g],
OO [auth s],
OP [auth y],
OR [auth C1],
OU [auth G1],
OW [auth Y1],
OX [auth b1],
OY [auth c1],
OZ [auth d1],
PAA [auth n1],
PCA [auth s1],
PD [auth B],
PE [auth C],
PG [auth G],
PH [auth R],
PJ [auth a],
PN [auth g],
PP [auth y],
PQ [auth B1],
PR [auth C1],
PS [auth D1],
PW [auth Y1],
PX [auth b1],
PY [auth c1],
PZ [auth d1],
QAA [auth n1],
QCA [auth s1],
QD [auth B],
QE [auth C],
QG [auth G],
QH [auth R],
QI [auth Y],
QN [auth g],
QP [auth y],
QQ [auth B1],
QR [auth C1],
QS [auth D1],
QV [auth S1],
QW [auth Y1],
QX [auth b1],
QY [auth c1],
RAA [auth n1],
RBA [auth r1],
RCA [auth s1],
RD [auth B],
RE [auth C],
RI [auth Y],
RP [auth y],
RQ [auth B1],
RR [auth C1],
RT [auth N1],
RV [auth S1],
RX [auth b1],
RY [auth c1],
SAA [auth n1],
SBA [auth r1],
SCA [auth s1],
SD [auth B],
SE [auth C],
SI [auth Y],
SJ [auth a],
SO [auth s],
SP [auth y],
SQ [auth B1],
SR [auth C1],
ST [auth N1],
SV [auth S1],
SX [auth b1],
SY [auth c1],
TBA [auth r1],
TCA [auth s1],
TD [auth B],
TM [auth n],
TO [auth s],
TQ [auth B1],
TR [auth C1],
TT [auth N1],
TV [auth S1],
TX [auth b1],
TY [auth c1],
UD [auth B],
UM [auth n],
UO [auth s],
UQ [auth B1],
UR [auth C1],
UT [auth N1],
UU [auth R1],
UV [auth S1],
UX [auth b1],
UY [auth c1],
VD [auth B],
VF [auth N],
VH [auth S],
VK [auth c],
VM [auth n],
VO [auth s],
VQ [auth B1],
VR [auth C1],
VT [auth N1],
VU [auth R1],
VV [auth S1],
VX [auth b1],
VY [auth c1],
WBA [auth r1],
WD [auth B],
WF [auth N],
WG [auth G],
WH [auth S],
WI [auth Y],
WK [auth c],
WL [auth d],
WM [auth n],
WO [auth s],
WQ [auth B1],
WR [auth C1],
WU [auth R1],
WV [auth S1],
WX [auth b1],
WY [auth c1],
XBA [auth r1],
XD [auth B],
XF [auth N],
XG [auth G],
XH [auth S],
XJ [auth b],
XK [auth c],
XL [auth d],
XM [auth n],
XO [auth s],
XQ [auth B1],
XR [auth C1],
XX [auth b1],
XY [auth c1],
YBA [auth r1],
YD [auth B],
YG [auth G],
YH [auth S],
YI [auth Y],
YJ [auth b],
YK [auth c],
YO [auth s],
YQ [auth B1],
YR [auth C1],
YX [auth b1],
YY [auth c1],
ZAA [auth g1],
ZBA [auth r1],
ZC [auth A],
ZG [auth G],
ZI [auth Y],
ZJ [auth b],
ZK [auth c],
ZN [auth r],
ZQ [auth B1],
ZR [auth C1],
ZU [auth R1],
ZX [auth b1],
ZY [auth c1]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
CD [auth A]
DD [auth A]
GX [auth a1]
HQ [auth A1]
HX [auth a1]
CD [auth A],
DD [auth A],
GX [auth a1],
HQ [auth A1],
HX [auth a1],
IQ [auth A1],
QJ [auth a],
RJ [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
4RF

Query on 4RF



Download:Ideal Coordinates CCD File
BAA [auth k1],
BT [auth I1],
DT [auth K1],
ZZ [auth i1]
Tripalmitoylglycerol
C51 H98 O6
PVNIQBQSYATKKL-UHFFFAOYSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
CAA [auth m1]
CE [auth B]
EF [auth C]
FT [auth M1]
GD [auth A]
CAA [auth m1],
CE [auth B],
EF [auth C],
FT [auth M1],
GD [auth A],
HY [auth b1],
IR [auth B1],
KX [auth a1],
LQ [auth A1],
LZ [auth c1],
MS [auth C1],
MY [auth b1],
NR [auth B1],
QK [auth b],
TL [auth c],
UJ [auth a]
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
AF [auth C]
DE [auth B]
DM [auth d]
EAA [auth w1]
GM [auth h]
AF [auth C],
DE [auth B],
DM [auth d],
EAA [auth w1],
GM [auth h],
HD [auth A],
HT [auth W1],
HZ [auth c1],
IM [auth j],
IS [auth C1],
IY [auth b1],
IZ [auth c1],
JR [auth B1],
JS [auth C1],
LX [auth a1],
MQ [auth A1],
OF [auth D],
PL [auth c],
RF [auth H],
RK [auth b],
SF [auth J],
VJ [auth a],
VZ [auth d1],
WS [auth D1],
YZ [auth h1],
ZS [auth H1]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LMK

Query on LMK



Download:Ideal Coordinates CCD File
FF [auth C],
MZ [auth c1],
NS [auth C1],
UL [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
KF [auth D],
RZ [auth d1],
SS [auth D1],
ZL [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
UDA [auth y1],
VDA [auth y1],
XW [auth Y1],
YW [auth Y1]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
AM [auth d]
AU [auth N1]
AW [auth S1]
BM [auth d]
CM [auth d]
AM [auth d],
AU [auth N1],
AW [auth S1],
BM [auth d],
CM [auth d],
CN [auth n],
CP [auth s],
DF [auth C],
ET [auth L1],
FH [auth G],
HJ [auth Y],
JM [auth l],
KZ [auth c1],
LF [auth D],
LS [auth C1],
MF [auth D],
MG [auth N],
MI [auth S],
NF [auth D],
QBA [auth g1],
SDA [auth y1],
SL [auth c],
SZ [auth d1],
TF [auth L],
TS [auth D1],
TU [auth G1],
TZ [auth d1],
US [auth D1],
UZ [auth d1],
VN [auth g],
VS [auth D1],
VW [auth Y1],
XAA [auth n1],
XCA [auth s1],
XP [auth y]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH

Query on 3PH



Download:Ideal Coordinates CCD File
CW [auth S1]
DAA [auth t1]
EP [auth s]
GT [auth T1]
HM [auth i]
CW [auth S1],
DAA [auth t1],
EP [auth s],
GT [auth T1],
HM [auth i],
KY [auth b1],
LR [auth B1],
OI [auth S],
ZCA [auth s1]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA

Query on DGA



Download:Ideal Coordinates CCD File
AAA [auth j1]
CF [auth C]
CT [auth J1]
EE [auth B]
JZ [auth c1]
AAA [auth j1],
CF [auth C],
CT [auth J1],
EE [auth B],
JZ [auth c1],
KS [auth C1],
LY [auth b1],
MR [auth B1],
RL [auth c],
SK [auth b]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
EM [auth f],
PF [auth F],
WZ [auth f1],
XS [auth F1]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NEX

Query on NEX



Download:Ideal Coordinates CCD File
BN [auth n]
BP [auth s]
CCA [auth r1]
EH [auth G]
FV [auth R1]
BN [auth n],
BP [auth s],
CCA [auth r1],
EH [auth G],
FV [auth R1],
GJ [auth Y],
LG [auth N],
LI [auth S],
PBA [auth g1],
RDA [auth y1],
SU [auth G1],
TH [auth R],
UN [auth g],
UW [auth Y1],
WAA [auth n1],
WCA [auth s1],
WP [auth y],
YN [auth r],
ZT [auth N1],
ZV [auth S1]
(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
AN [auth n]
BCA [auth r1]
DH [auth G]
EV [auth R1]
FJ [auth Y]
AN [auth n],
BCA [auth r1],
DH [auth G],
EV [auth R1],
FJ [auth Y],
KG [auth N],
OBA [auth g1],
QDA [auth y1],
RU [auth G1],
SH [auth R],
TN [auth g],
TW [auth Y1],
VAA [auth n1],
VP [auth y],
XN [auth r],
YT [auth N1]
(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
ACA [auth r1]
AP [auth s]
BH [auth G]
CH [auth G]
DJ [auth Y]
ACA [auth r1],
AP [auth s],
BH [auth G],
CH [auth G],
DJ [auth Y],
DV [auth R1],
EJ [auth Y],
IG [auth N],
JG [auth N],
JI [auth S],
KI [auth S],
MBA [auth g1],
NBA [auth g1],
ODA [auth y1],
PDA [auth y1],
PU [auth G1],
QU [auth G1],
RH [auth R],
RN [auth g],
RW [auth Y1],
SN [auth g],
SW [auth Y1],
TAA [auth n1],
TP [auth y],
UAA [auth n1],
UCA [auth s1],
UP [auth y],
VCA [auth s1],
WN [auth r],
WT [auth N1],
XT [auth N1],
XV [auth S1],
YM [auth n],
YV [auth S1],
ZM [auth n],
ZO [auth s]
(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
BE [auth B],
GY [auth b1],
HR [auth B1],
PK [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
FM [auth h],
QF [auth H],
XZ [auth h1],
YS [auth H1]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AE [auth B]
AZ [auth c1]
BS [auth C1]
BZ [auth c1]
CS [auth C1]
AE [auth B],
AZ [auth c1],
BS [auth C1],
BZ [auth c1],
CS [auth C1],
CZ [auth c1],
DS [auth C1],
DZ [auth c1],
ES [auth C1],
EY [auth b1],
FD [auth A],
FR [auth B1],
FY [auth b1],
GR [auth B1],
IL [auth c],
JF [auth D],
JL [auth c],
JX [auth a1],
KL [auth c],
KQ [auth A1],
LL [auth c],
NK [auth b],
OK [auth b],
QZ [auth d1],
RS [auth D1],
TE [auth C],
TJ [auth a],
UE [auth C],
VE [auth C],
WE [auth C],
YL [auth d],
ZD [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
DCA [auth r1],
GV [auth R1]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LPX

Query on LPX



Download:Ideal Coordinates CCD File
BW [auth S1],
DP [auth s],
NI [auth S],
YCA [auth s1]
(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
ECA [auth r1],
HV [auth R1]
ERGOSTEROL
C28 H44 O
DNVPQKQSNYMLRS-APGDWVJJSA-N
OEX

Query on OEX



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

Query on SPH



Download:Ideal Coordinates CCD File
IJ [auth Y]
MX [auth a1]
NQ [auth A1]
TDA [auth y1]
WW [auth Y1]
IJ [auth Y],
MX [auth a1],
NQ [auth A1],
TDA [auth y1],
WW [auth Y1],
YP [auth y]
SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AT [auth I1],
FE [auth B],
TK [auth b],
UK [auth b],
ZP [auth y]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
GF [auth D],
NZ [auth d1],
OS [auth D1],
VL [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



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

Query on CL



Download:Ideal Coordinates CCD File
BX [auth a1]
CQ [auth A1]
CX [auth a1]
DQ [auth A1]
LJ [auth a]
BX [auth a1],
CQ [auth A1],
CX [auth a1],
DQ [auth A1],
LJ [auth a],
MJ [auth a],
XC [auth A],
YC [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
ID [auth A],
NX [auth a1],
OQ [auth A1],
WJ [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]
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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: 2024-10-16
    Changes: Data collection, Refinement description, Structure summary