7PNK

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


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 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,
Y [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 proteinB,
Z [auth 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 Ycf12AA [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 proteinBA [auth c],
D [auth C]		449Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
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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 
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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 
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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 
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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 
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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 
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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 
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Find proteins for A0A1C8XRM8 (Dunaliella salina)
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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 
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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 
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Find proteins for D0FY19 (Dunaliella salina)
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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 
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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 
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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 
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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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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 
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Small Molecules
Ligands 27 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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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
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PD [auth H],
ZJ [auth h]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR
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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
Download Ideal Coordinates CCD File 
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



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: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary