7PNK

Unstacked compact Dunaliella PSII

• PDB DOI: https://doi.org/10.2210/pdb7PNK/pdb
• EM Map EMD-13548: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Dunaliella salina
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2021-09-07 Released: 2022-08-17 
• Deposition Author(s): Caspy, I., Fadeeva, M., Mazor, Y., Nelson, N.
• Funding Organization(s): Israel Science Foundation

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 36799903 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 44-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V1W1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 44-mer - A11B4C4D4E2F2G2H2I2J2K2L2M2N2O1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 40-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2U2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 40-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2U2 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	A, Y [auth a]	336	Dunaliella salina	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for D0FY08 (Dunaliella salina) Explore D0FY08  Go to UniProtKB:  D0FY08

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	B, Z [auth b]	484	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A1C8XRM6 (Dunaliella salina) Explore A0A1C8XRM6  Go to UniProtKB:  A0A1C8XRM6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Ycf12	AA [auth v], C [auth V]	32	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0FY13 (Dunaliella salina) Explore D0FY13  Go to UniProtKB:  D0FY13

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	BA [auth c], D [auth C]	449	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0FXY3 (Dunaliella salina) Explore D0FXY3  Go to UniProtKB:  D0FXY3

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	CA [auth d], E [auth D]	348	Dunaliella salina	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for A0A1C8XRK9 (Dunaliella salina) Explore A0A1C8XRK9  Go to UniProtKB:  A0A1C8XRK9

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	DA [auth e], F [auth E]	76	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0FY01 (Dunaliella salina) Explore D0FY01  Go to UniProtKB:  D0FY01

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	EA [auth f], G [auth F]	31	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A1C8XRP4 (Dunaliella salina) Explore A0A1C8XRP4  Go to UniProtKB:  A0A1C8XRP4

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	FA [auth h], H	67	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A1C8XRP3 (Dunaliella salina) Explore A0A1C8XRP3  Go to UniProtKB:  A0A1C8XRP3

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	GA [auth i], I	35	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0FXX5 (Dunaliella salina) Explore D0FXX5  Go to UniProtKB:  D0FXX5

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	HA [auth j], J	36	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A1C8XRM8 (Dunaliella salina) Explore A0A1C8XRM8  Go to UniProtKB:  A0A1C8XRM8

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	IA [auth k], K	37	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0FXX2 (Dunaliella salina) Explore D0FXX2  Go to UniProtKB:  D0FXX2

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	JA [auth l], L	38	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0FY19 (Dunaliella salina) Explore D0FY19  Go to UniProtKB:  D0FY19

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	KA [auth m], M	31	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0FXZ3 (Dunaliella salina) Explore D0FXZ3  Go to UniProtKB:  D0FXZ3

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbO	LA [auth o], N [auth O]	238	Dunaliella salina	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbP	MA [auth p], O [auth P]	187	Dunaliella salina	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	NA [auth t], P [auth T]	30	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0FY04 (Dunaliella salina) Explore D0FY04  Go to UniProtKB:  D0FY04

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbW	OA [auth w], Q [auth W]	44	Dunaliella salina	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbX	PA [auth x], R [auth X]	30	Dunaliella salina	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	QA [auth z], S [auth Z]	61	Dunaliella salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0FXZ2 (Dunaliella salina) Explore D0FXZ2  Go to UniProtKB:  D0FXZ2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein of LHCII type I, chloroplastic	T [auth N]	222	Dunaliella salina	Mutation(s): 0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	U [auth G]	221	Dunaliella salina	Mutation(s): 0
UniProt
Find proteins for A1XKU7 (Dunaliella salina) Explore A1XKU7  Go to UniProtKB:  A1XKU7

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
CP26	V [auth S]	243	Dunaliella salina	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
LHCII M1	W [auth Y]	222	Dunaliella salina	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbU	RA [auth u], X [auth U]	27	Dunaliella salina	Mutation(s): 0

Small Molecules

Ligands 27 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	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	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	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	AB [auth A], JH [auth a], KH [auth a], ZA [auth A]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
4RF	BK [auth i], DK [auth k], SD [auth I], UD [auth K]	Tripalmitoylglycerol C51 H98 O6 PVNIQBQSYATKKL-UHFFFAOYSA-N
SQD	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	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	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	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	AH [auth Y], BH [auth Y]	PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG	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	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	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	OD [auth F], YJ [auth f]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NEX	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	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	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	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	PD [auth H], ZJ [auth h]	(3R)-beta,beta-caroten-3-ol C40 H56 O DMASLKHVQRHNES-FKKUPVFPSA-N
BCR	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	EG [auth S]	(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate C21 H44 N O7 P YVYMBNSKXOXSKW-FQEVSTJZSA-N
OEX	CH [auth a], SA [auth A]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
SPH	FB [auth A], PH [auth a], ZG [auth Y]	SPHINGOSINE C18 H37 N O2 WWUZIQQURGPMPG-MSOLQXFVSA-N
GOL	RD [auth I]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT	FD [auth D], PJ [auth d]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	DH [auth a], TA [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	EH [auth a], FH [auth a], UA [auth A], VA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	B, Z [auth b]	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-17 
Deposition Author(s): Caspy, I., Fadeeva, M., Mazor, Y., Nelson, N.

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Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	569/17
Israel Science Foundation	Israel	199/21

Revision History  

• 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