7PI0

Unstacked compact Dunaliella PSII

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
Z [auth a]		336Dunaliella salinaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinAA [auth b],
B		484Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRM6 (Dunaliella salina)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12BA [auth v],
C [auth V]		32Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY13 (Dunaliella salina)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinCA [auth c],
D [auth C]		449Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for D0FXY3 (Dunaliella salina)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinDA [auth d],
E [auth D]		348Dunaliella salinaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaEA [auth e],
F [auth E]		76Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaFA [auth f],
G [auth F]		31Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HGA [auth h],
H		67Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IHA [auth i],
I		35Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for D0FXX5 (Dunaliella salina)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JIA [auth j],
J		36Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRM8 (Dunaliella salina)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJA [auth k],
K		37Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LKA [auth l],
L		38Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PsbMLA [auth m],
M		31Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PsbOMA [auth o],
N [auth O]		238Dunaliella salinaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PsbPNA [auth p],
O [auth P]		187Dunaliella salinaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TOA [auth t],
P [auth T]		30Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PsbWPA [auth w],
Q [auth W]		44Dunaliella salinaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PsbXQA [auth x],
R [auth X]		30Dunaliella salinaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZRA [auth z],
S [auth Z]		61Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
LHCII M3SA [auth n],
T [auth N]		222Dunaliella salinaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticTA [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
CP29UA [auth r],
V [auth R]		196Dunaliella salinaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
CP26VA [auth s],
W [auth S]		243Dunaliella salinaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
LHCII M1WA [auth y],
X [auth Y]		222Dunaliella salinaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
PsbUXA [auth u],
Y [auth U]		27Dunaliella salinaMutation(s): 0 
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Small Molecules
Ligands 26 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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CD [auth C]
DD [auth C]
ED [auth C]
GJ [auth b]
HC [auth B]
CD [auth C],
DD [auth C],
ED [auth C],
GJ [auth b],
HC [auth B],
XJ [auth c],
YJ [auth c],
ZJ [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL
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AH [auth Y]
AM [auth g]
AO [auth y]
BF [auth G]
BO [auth y]
AH [auth Y],
AM [auth g],
AO [auth y],
BF [auth G],
BO [auth y],
CF [auth G],
CG [auth S],
CL [auth n],
CN [auth s],
DE [auth N],
DF [auth G],
DL [auth n],
DN [auth s],
DO [auth y],
EF [auth G],
EH [auth Y],
EL [auth n],
EN [auth s],
FF [auth G],
FH [auth Y],
FL [auth n],
GH [auth Y],
HE [auth N],
HG [auth S],
IE [auth N],
IG [auth S],
IH [auth Y],
JE [auth N],
JG [auth S],
KE [auth N],
LE [auth N],
OM [auth r],
PL [auth n],
PM [auth r],
SL [auth g],
TF [auth R],
UF [auth R],
VN [auth y],
WL [auth g],
XE [auth G],
XL [auth g],
XM [auth s],
YK [auth n],
YL [auth g],
ZL [auth g],
ZN [auth y]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA
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AC [auth B]
AF [auth G]
AI [auth a]
AL [auth n]
AN [auth s]
AC [auth B],
AF [auth G],
AI [auth a],
AL [auth n],
AN [auth s],
BC [auth B],
BH [auth Y],
BL [auth n],
BM [auth g],
BN [auth s],
CB [auth A],
CC [auth B],
CH [auth Y],
CM [auth g],
CO [auth y],
DB [auth A],
DG [auth S],
DH [auth Y],
DM [auth g],
EB [auth A],
EE [auth N],
EG [auth S],
EM [auth g],
EO [auth y],
FE [auth N],
FG [auth S],
FM [auth g],
FN [auth s],
FO [auth y],
GB [auth A],
GE [auth N],
GF [auth G],
GG [auth S],
GL [auth n],
GN [auth s],
GO [auth y],
HF [auth G],
HH [auth Y],
HL [auth n],
HN [auth s],
HO [auth y],
IF [auth G],
IJ [auth c],
IL [auth n],
IN [auth s],
IO [auth y],
JF [auth G],
JH [auth Y],
JI [auth b],
JJ [auth c],
JL [auth n],
JN [auth s],
KF [auth G],
KG [auth S],
KH [auth Y],
KI [auth b],
KJ [auth c],
KK [auth d],
KL [auth n],
KN [auth s],
LG [auth S],
LH [auth Y],
LI [auth b],
LJ [auth c],
LK [auth d],
LM [auth r],
LN [auth s],
MC [auth C],
ME [auth N],
MG [auth S],
MH [auth Y],
MI [auth b],
MJ [auth c],
MM [auth r],
NB [auth B],
NC [auth C],
ND [auth D],
NE [auth N],
NG [auth S],
NH [auth Y],
NI [auth b],
NJ [auth c],
NM [auth r],
OB [auth B],
OC [auth C],
OD [auth D],
OE [auth N],
OG [auth S],
OI [auth b],
OJ [auth c],
PB [auth B],
PC [auth C],
PE [auth N],
PG [auth S],
PI [auth b],
PJ [auth c],
QB [auth B],
QC [auth C],
QE [auth N],
QF [auth R],
QG [auth S],
QI [auth b],
QJ [auth c],
QM [auth r],
RB [auth B],
RC [auth C],
RF [auth R],
RI [auth b],
RJ [auth c],
RM [auth r],
SB [auth B],
SC [auth C],
SF [auth R],
SI [auth b],
SJ [auth c],
SM [auth r],
TB [auth B],
TC [auth C],
TI [auth b],
TJ [auth c],
TL [auth g],
TM [auth r],
UB [auth B],
UC [auth C],
UI [auth b],
UJ [auth c],
UL [auth g],
VB [auth B],
VC [auth C],
VF [auth R],
VI [auth b],
VL [auth g],
WB [auth B],
WC [auth C],
WF [auth R],
WH [auth a],
WI [auth b],
WN [auth y],
XB [auth B],
XC [auth C],
XF [auth R],
XH [auth a],
XI [auth b],
XN [auth y],
YB [auth B],
YC [auth C],
YE [auth G],
YF [auth R],
YH [auth a],
YI [auth b],
YM [auth s],
YN [auth y],
ZB [auth B],
ZE [auth G],
ZK [auth n],
ZM [auth s]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO
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FB [auth A],
FI [auth a],
KB [auth A],
ZH [auth a]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD
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AE [auth M]
CI [auth a]
DK [auth c]
FJ [auth b]
HD [auth C]
AE [auth M],
CI [auth a],
DK [auth c],
FJ [auth b],
HD [auth C],
II [auth b],
JB [auth A],
KC [auth B],
LC [auth B],
VK [auth m]
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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AK [auth c]
BK [auth c]
CE [auth W]
CJ [auth b]
FD [auth C]
AK [auth c],
BK [auth c],
CE [auth W],
CJ [auth b],
FD [auth C],
GC [auth B],
GD [auth C],
GI [auth a],
ID [auth C],
MB [auth A],
OK [auth d],
RK [auth h],
TD [auth D],
WD [auth H],
XK [auth w]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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MK [auth d],
PD [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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NO [auth y],
SH [auth Y],
TN [auth y],
YG [auth Y]		PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG
Query on LHG
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CK [auth c]
GK [auth c]
IK [auth d]
JK [auth d]
JM [auth g]
CK [auth c],
GK [auth c],
IK [auth d],
JK [auth d],
JM [auth g],
LD [auth C],
MO [auth y],
NK [auth d],
OF [auth G],
OL [auth n],
PN [auth s],
QD [auth D],
RD [auth D],
RH [auth Y],
SD [auth D],
UE [auth N],
UG [auth S],
UK [auth l],
ZD [auth L]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH
Query on 3PH
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BE [auth T]
DJ [auth b]
IC [auth B]
RN [auth s]
WG [auth S]
BE [auth T],
DJ [auth b],
IC [auth B],
RN [auth s],
WG [auth S],
WK [auth t]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA
Query on DGA
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EJ [auth b]
EK [auth c]
JC [auth B]
KD [auth C]
TK [auth j]
EJ [auth b],
EK [auth c],
JC [auth B],
KD [auth C],
TK [auth j],
YD [auth J]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEM
Query on HEM
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QK [auth f],
VD [auth F]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
XAT
Query on XAT
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AG [auth R]
QL [auth n]
RL [auth g]
UN [auth y]
VE [auth N]
AG [auth R],
QL [auth n],
RL [auth g],
UN [auth y],
VE [auth N],
VM [auth r],
WE [auth G],
ZG [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
NEX
Query on NEX
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BG [auth R]
IM [auth g]
LO [auth y]
NF [auth G]
NL [auth n]
BG [auth R],
IM [auth g],
LO [auth y],
NF [auth G],
NL [auth n],
ON [auth s],
QH [auth Y],
TE [auth N],
TG [auth S],
WM [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
LUT
Query on LUT
Download Ideal Coordinates CCD File 
GM [auth g]
HM [auth g]
JO [auth y]
KO [auth y]
LF [auth G]
GM [auth g],
HM [auth g],
JO [auth y],
KO [auth y],
LF [auth G],
LL [auth n],
MF [auth G],
ML [auth n],
MN [auth s],
NN [auth s],
OH [auth Y],
PH [auth Y],
RE [auth N],
RG [auth S],
SE [auth N],
SG [auth S],
UM [auth r],
ZF [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 
BJ [auth b],
FC [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 
SK [auth h],
XD [auth H]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR
Download Ideal Coordinates CCD File 
AD [auth C]
AJ [auth b]
BD [auth C]
BI [auth a]
DC [auth B]
AD [auth C],
AJ [auth b],
BD [auth C],
BI [auth a],
DC [auth B],
EC [auth B],
FK [auth c],
HB [auth A],
HJ [auth c],
JD [auth C],
PK [auth d],
UD [auth D],
VJ [auth c],
WJ [auth c],
ZC [auth C],
ZI [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
Download Ideal Coordinates CCD File 
KM [auth r],
PF [auth R]		DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LPX
Query on LPX
Download Ideal Coordinates CCD File 
QN [auth s],
VG [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 
TH [auth a],
YA [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
SPH
Query on SPH
Download Ideal Coordinates CCD File 
HI [auth a],
LB [auth A],
SN [auth y],
XG [auth Y]		SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
BCT
Query on BCT
Download Ideal Coordinates CCD File 
HK [auth d],
MD [auth D]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
Download Ideal Coordinates CCD File 
EI [auth a],
ZA [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
AB [auth A],
BB [auth A],
UH [auth a],
VH [auth a]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA
Download Ideal Coordinates CCD File 
DI [auth a],
IB [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD		AA [auth b],
B		L-PEPTIDE LINKINGC3 H7 N O4 SCYS
SEP
Query on SEP		UA [auth r],
V [auth R]		L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.43 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 2.0: 2022-12-21
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2023-03-01
    Changes: Database references