8GN1

Crystal structure of DBBQ-bound photosystem II complex

• PDB DOI: https://doi.org/10.2210/pdb8GN1/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Thermostichus vulcanus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2022-08-22 Released: 2023-07-05 
• Deposition Author(s): Kamada, S., Nakajima, Y., Shen, J.-R.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.191 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Structural insights into the action mechanisms of artificial electron acceptors in photosystem II.

Kamada, S., Nakajima, Y., Shen, J.R.

(2023) J Biol Chem 299: 104839-104839

• PubMed: 37209822 
• DOI: https://doi.org/10.1016/j.jbc.2023.104839
• Primary Citation of Related Structures:  
  8GN0, 8GN1, 8GN2


• PubMed Abstract: 
  

  Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to Q _B , a plastoquinone molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with molecular structures similar to that of plastoquinone can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95 to 2.10 Å resolution. Our results show that all AEAs substitute for Q _B and are bound to the Q _B -binding site (Q _B site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the Q _B site and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone-binding site, designated the Q _D site, was discovered, which is located in the vicinity of Q _B site and close to Q _C site, a binding site reported previously. This Q _D site is expected to play a role as a channel or a storage site for quinones to be transported to the Q _B site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of Q _B in PSII and also provide information for the design of more efficient electron acceptors.

---

Organizational Affiliation: 

Faculty of Science, Okayama University, Okayama, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 39-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 39-mer - A9B4C2D2E2F2G2H2I2J2K2L2M2N2O1P1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 38-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 38-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 752.73 kDa 
• Atom Count: 54,282 
• Modelled Residue Count: 5,284 
• Deposited Residue Count: 5,387 
• Unique protein chains: 20

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	A, T [auth a]	344	Thermostichus vulcanus	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for P51765 (Thermostichus vulcanus) Explore P51765  Go to UniProtKB:  P51765

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	B, U [auth b]	505	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus) Explore D0VWR1  Go to UniProtKB:  D0VWR1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	C, V [auth c]	455	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR7 (Thermostichus vulcanus) Explore D0VWR7  Go to UniProtKB:  D0VWR7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D, W [auth d]	342	Thermostichus vulcanus	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for D0VWR8 (Thermostichus vulcanus) Explore D0VWR8  Go to UniProtKB:  D0VWR8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E, X [auth e]	83	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12238 (Thermostichus vulcanus) Explore P12238  Go to UniProtKB:  P12238

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F, Y [auth f]	44	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12239 (Thermostichus vulcanus) Explore P12239  Go to UniProtKB:  P12239

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	G [auth H], Z [auth h]	63	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P19052 (Thermostichus vulcanus) Explore P19052  Go to UniProtKB:  P19052

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	AA [auth i], H [auth I]	38	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12240 (Thermostichus vulcanus) Explore P12240  Go to UniProtKB:  P12240

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	BA [auth j], I [auth J]	40	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q7DGD4 (Thermostichus vulcanus) Explore Q7DGD4  Go to UniProtKB:  Q7DGD4

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	CA [auth k], J [auth K]	37	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P19054 (Thermostichus vulcanus) Explore P19054  Go to UniProtKB:  P19054

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	DA [auth l], K [auth L]	37	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12241 (Thermostichus vulcanus) Explore P12241  Go to UniProtKB:  P12241

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	EA [auth m], L [auth M]	36	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12312 (Thermostichus vulcanus) Explore P12312  Go to UniProtKB:  P12312

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II manganese-stabilizing polypeptide	FA [auth o], M [auth O]	244	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR2 (Thermostichus vulcanus) Explore D0VWR2  Go to UniProtKB:  D0VWR2

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	GA [auth t], N [auth T]	32	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12313 (Thermostichus vulcanus) Explore P12313  Go to UniProtKB:  P12313

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 12 kDa extrinsic protein	HA [auth u], O [auth U]	104	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P56152 (Thermostichus vulcanus) Explore P56152  Go to UniProtKB:  P56152

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	IA [auth v], P [auth V]	137	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A387 (Thermostichus vulcanus) Explore P0A387  Go to UniProtKB:  P0A387

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Ycf12	JA [auth y], Q [auth Y]	30	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus) Explore D0VWR3  Go to UniProtKB:  D0VWR3

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein X	KA [auth x], R [auth X]	40	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus) Explore D0VWR4  Go to UniProtKB:  D0VWR4

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	LA [auth z], S [auth Z]	62	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus) Explore D0VWR5  Go to UniProtKB:  D0VWR5

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein Y	MA [auth R]	41	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0DM37 (Thermostichus vulcanus) Explore P0DM37  Go to UniProtKB:  P0DM37

Small Molecules

Ligands 23 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	BE [auth C], CE [auth C], DE [auth C], EG [auth H], FF [auth D], KL [auth c], LL [auth c], ML [auth c], ON [auth h]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AC [auth B], AL [auth c], BC [auth B], BF [auth D], BL [auth c], CC [auth B], CF [auth D], CL [auth c], DC [auth B], DL [auth c], EL [auth c], FJ [auth b], FL [auth c], GJ [auth b], GL [auth c], HJ [auth b], HL [auth c], IJ [auth b], JJ [auth b], JM [auth d], KJ [auth b], LJ [auth b], MD [auth C], MI [auth a], MJ [auth b], MM [auth d], ND [auth C], NI [auth a], NJ [auth b], NM [auth d], OB [auth B], OD [auth C], OJ [auth b], PB [auth B], PD [auth C], PJ [auth b], QB [auth B], QD [auth C], QI [auth a], QJ [auth b], RA [auth A], RB [auth B], RD [auth C], RJ [auth b], SA [auth A], SB [auth B], SD [auth C], SJ [auth b], TB [auth B], TD [auth C], TJ [auth b], UB [auth B], UD [auth C], UJ [auth b], VA [auth A], VB [auth B], VD [auth C], VK [auth c], WB [auth B], WD [auth C], WK [auth c], XB [auth B], XD [auth C], XK [auth c], YB [auth B], YD [auth C], YE [auth D], YK [auth c], ZB [auth B], ZK [auth c]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	OI [auth a], PI [auth a], TA [auth A], UA [auth A]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	AG [auth F], FI [auth a], HC [auth B], LN [auth f], PG [auth L], SI [auth a], XA [auth A], ZA [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	EE [auth C], IC [auth B], JF [auth D], KE [auth C], NL [auth c], OL [auth c], QN [auth i], TM [auth d], YA [auth A], YJ [auth b]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)	DB [auth A], EF [auth D], PM [auth d], PP [auth x]	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
LHG	EO [auth l], GF [auth D], GN [auth e], HF [auth D], IF [auth D], OG [auth L], QM [auth d], RM [auth d], SF [auth E], SM [auth d]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC	BP [auth v], PH [auth V]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM	BG [auth F], IN [auth e]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
RRX	DG [auth H], NN [auth h]	(3R)-beta,beta-caroten-3-ol C40 H56 O DMASLKHVQRHNES-FKKUPVFPSA-N
BCR	AE [auth C], AI [auth Y], CO [auth k], DF [auth D], EC [auth B], FC [auth B], GC [auth B], GH [auth T], IL [auth c], JL [auth c], NG [auth K], OM [auth d], RI [auth a], UL [auth c], VJ [auth b], VO [auth t], WA [auth A], WJ [auth b], XJ [auth b], ZD [auth C]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	AB [auth A], CI [auth Z], GB [auth A], GG [auth I], GI [auth a], GO [auth m], HH [auth T], HO [auth m], JC [auth B], KN [auth f], LG [auth J], QG [auth M], RP [auth z], TN [auth i], WC [auth B], WF [auth E], WN [auth j], XC [auth B], XI [auth a], ZJ [auth b]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX	HI [auth a], NA [auth A]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG	AK [auth b], BK [auth b], CJ [auth b], DJ [auth b], FE [auth C], GE [auth C], HG [auth I], KC [auth B], KF [auth D], LC [auth B], LM [auth d], MC [auth B], NC [auth B], OC [auth B], PL [auth c], QL [auth c], SH [auth V], SL [auth c], SN [auth i], TG [auth O], WM [auth d]	heptyl 1-thio-beta-D-glucopyranoside C13 H26 O5 S HPEGNLMTTNTJSP-LBELIVKGSA-N
K2I (Subject of Investigation/LOI)	EB [auth A], FB [auth A], VI [auth a], WI [auth a]	2,5-bis(bromanyl)cyclohexa-2,5-diene-1,4-dione C6 H2 Br2 O2 KNPAQJBQOIAPBP-UHFFFAOYSA-N
GOL	AF [auth D], AO [auth k], CP [auth v], DI [auth Z], DP [auth v], EI [auth a], EP [auth v], FG [auth H], GK [auth b], IE [auth C], IO [auth o], JE [auth C], KO [auth o], MH [auth U], NH [auth U], RH [auth V], SC [auth B], TL [auth c], UG [auth O], VC [auth B], XM [auth d]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	AD [auth B], AH [auth O], AJ [auth a], AM [auth c], AN [auth d], AP [auth u], BD [auth B], BH [auth O], BJ [auth a], BM [auth c], BN [auth d], CD [auth B], CG [auth F], CH [auth O], CM [auth c], CN [auth d], DD [auth B], DH [auth O], DM [auth c], DN [auth d], DO [auth k], ED [auth B], EH [auth O], EM [auth c], EN [auth d], FD [auth B], FH [auth O], FM [auth c], FN [auth d], FP [auth v], GD [auth B], GM [auth c], GP [auth v], HD [auth B], HK [auth b], HM [auth c], HP [auth v], IB [auth A], ID [auth B], IK [auth b], IM [auth c], IP [auth v], JB [auth A], JD [auth B], JH [auth T], JK [auth b], JN [auth e], JP [auth v], KB [auth A], KD [auth B], KH [auth T], KK [auth b], KP [auth v], LB [auth A], LE [auth C], LH [auth T], LK [auth b], LO [auth o], LP [auth v], MB [auth A], ME [auth C], MK [auth b], MO [auth o], MP [auth v], NE [auth C], NF [auth D], NK [auth b], NO [auth o], NP [auth v], OE [auth C], OF [auth D], OH [auth U], OK [auth b], OO [auth o], OP [auth v], PE [auth C], PF [auth D], PK [auth b], PO [auth o], QE [auth C], QF [auth D], QH [auth V], QK [auth b], QO [auth o], QP [auth x], RE [auth C], RF [auth D], RK [auth b], RO [auth o], SE [auth C], SK [auth b], SO [auth o], SP [auth z], TE [auth C], TH [auth V], TO [auth o], UE [auth C], UH [auth V], VE [auth C], VG [auth O], VH [auth V], VL [auth c], VN [auth i], WE [auth C], WG [auth O], WH [auth V], WL [auth c], WO [auth t], XE [auth C], XG [auth O], XH [auth V], XL [auth c], XO [auth u], YC [auth B], YF [auth E], YG [auth O], YH [auth V], YI [auth a], YL [auth c], YO [auth u], ZC [auth B], ZF [auth E], ZG [auth O], ZI [auth a], ZL [auth c], ZM [auth d], ZN [auth j], ZO [auth u]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)	HB [auth A], LI [auth a]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2 (Subject of Investigation/LOI)	II [auth a], OA [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CA	EJ [auth b], JO [auth o], NB [auth B], SG [auth O], UK [auth c]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	JI [auth a], KI [auth a], PA [auth A], QA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	KG [auth J], YN [auth j]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	BB [auth A], BI [auth X], BO [auth k], CB [auth A], CK [auth b], DK [auth b], EK [auth b], FK [auth b], FO [auth m], HE [auth C], HN [auth e], IG [auth I], IH [auth T], JG [auth I], KM [auth d], LD [auth C], LF [auth D], MF [auth D], MG [auth J], MN [auth h], PC [auth B], PN [auth h], QC [auth B], RC [auth B], RG [auth M], RL [auth c], RN [auth i], TC [auth B], TF [auth E], TI [auth a], TK [auth c], UC [auth B], UF [auth E], UI [auth a], UM [auth d], UN [auth i], UO [auth t], VF [auth E], VM [auth d], XF [auth E], XN [auth j], YM [auth d], ZE [auth D], ZH [auth Y]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HSK	D, W [auth d]	L-PEPTIDE LINKING	C6 H9 N3 O3		HIS
FME	AA [auth i], H [auth I]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.191 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.185	α = 90
b = 228.462	β = 90
c = 286.626	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Kamada, S., Nakajima, Y., Shen, J.-R.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Derived calculations, Refinement description