8GN2

Crystal structure of PPBQ-bound photosystem II complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
T [auth a]
344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]
505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]
455Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]
342Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]
83Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]
44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]
63Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]
38Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]
40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]
37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]
37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]
36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]
244Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]
32Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]
104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]
137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
Q [auth Y]
30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XKA [auth x],
R [auth X]
40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]
62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YMA [auth R]41Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKM3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Small Molecules
Ligands 23 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AK [auth c]
BK [auth c]
CK [auth c]
LF [auth H]
SE [auth D]
AK [auth c],
BK [auth c],
CK [auth c],
LF [auth H],
SE [auth D],
UL [auth h],
VD [auth C],
WD [auth C],
XD [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AC [auth B]
AI [auth b]
BI [auth b]
CI [auth b]
DI [auth b]
AC [auth B],
AI [auth b],
BI [auth b],
CI [auth b],
DI [auth b],
EH [auth a],
EI [auth b],
FH [auth a],
FI [auth b],
GD [auth C],
GH [auth a],
GI [auth b],
HD [auth C],
HI [auth b],
ID [auth C],
IH [auth a],
II [auth b],
JD [auth C],
JI [auth b],
KD [auth C],
KI [auth b],
LB [auth B],
LD [auth C],
LI [auth b],
LJ [auth c],
MB [auth B],
MD [auth C],
MI [auth b],
MJ [auth c],
NB [auth B],
ND [auth C],
NI [auth b],
NJ [auth c],
OB [auth B],
OD [auth C],
OE [auth D],
OI [auth b],
OJ [auth c],
PB [auth B],
PD [auth C],
PE [auth D],
PI [auth b],
PJ [auth c],
QB [auth B],
QD [auth C],
QJ [auth c],
RA [auth A],
RB [auth B],
RD [auth C],
RJ [auth c],
SA [auth A],
SB [auth B],
SD [auth C],
SJ [auth c],
TA [auth A],
TB [auth B],
TJ [auth c],
UB [auth B],
UJ [auth c],
VA [auth A],
VB [auth B],
VJ [auth c],
WB [auth B],
WJ [auth c],
XB [auth B],
XJ [auth c],
XK [auth d],
YB [auth B],
YK [auth d],
ZB [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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HH [auth a],
ME [auth D],
UA [auth A],
UK [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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KH [auth a]
NL [auth f]
TE [auth D]
WF [auth L]
XA [auth A]
KH [auth a],
NL [auth f],
TE [auth D],
WF [auth L],
XA [auth A],
XF [auth L],
XG [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
Query on LMG

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DK [auth c]
EC [auth B]
EK [auth c]
EL [auth d]
KE [auth C]
DK [auth c],
EC [auth B],
EK [auth c],
EL [auth d],
KE [auth C],
LH [auth a],
TI [auth b],
XE [auth D],
YA [auth A],
YD [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

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AL [auth d],
IB [auth A],
RE [auth D],
VH [auth a]
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
Query on LHG

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BL [auth d]
CF [auth E]
CL [auth d]
DL [auth d]
JM [auth l]
BL [auth d],
CF [auth E],
CL [auth d],
DL [auth d],
JM [auth l],
KL [auth e],
UE [auth D],
VE [auth D],
WE [auth D],
XC [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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BN [auth v],
MG [auth V]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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IF [auth F],
ML [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX
Query on RRX

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KF [auth H],
TL [auth h]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR

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BC [auth B]
CC [auth B]
DC [auth B]
FM [auth k]
GG [auth T]
BC [auth B],
CC [auth B],
DC [auth B],
FM [auth k],
GG [auth T],
GM [auth k],
JH [auth a],
QE [auth D],
QI [auth b],
RI [auth b],
SI [auth b],
TD [auth C],
TG [auth Y],
UD [auth C],
VF [auth K],
WA [auth A],
YC [auth B],
YJ [auth c],
ZJ [auth c],
ZK [auth d]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AB [auth A]
FC [auth B]
FF [auth E]
FK [auth c]
IG [auth T]
AB [auth A],
FC [auth B],
FF [auth E],
FK [auth c],
IG [auth T],
JN [auth z],
KM [auth m],
LM [auth m],
MM [auth m],
PL [auth f],
SF [auth J],
UI [auth b],
WG [auth Z],
YG [auth a],
ZC [auth B],
ZD [auth C],
ZF [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

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NA [auth A],
ZG [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG

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AE [auth C]
BE [auth C]
CG [auth O]
GC [auth B]
GK [auth c]
AE [auth C],
BE [auth C],
CG [auth O],
GC [auth B],
GK [auth c],
HC [auth B],
HK [auth c],
HL [auth d],
IC [auth B],
JC [auth B],
KG [auth U],
NG [auth V],
NM [auth o],
OF [auth I],
RL [auth h],
VI [auth b],
WI [auth b],
XH [auth b],
XM [auth u],
YE [auth D],
YH [auth b]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
K3C (Subject of Investigation/LOI)
Query on K3C

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HB [auth A],
UH [auth a]
2-phenylcyclohexa-2,5-diene-1,4-dione
C12 H8 O2
RLQZIECDMISZHS-UHFFFAOYSA-N
GOL
Query on GOL

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AG [auth M]
AJ [auth b]
AN [auth v]
BB [auth A]
CB [auth A]
AG [auth M],
AJ [auth b],
AN [auth v],
BB [auth A],
CB [auth A],
CE [auth C],
CN [auth v],
DG [auth O],
DN [auth v],
EN [auth v],
FE [auth C],
FG [auth T],
FN [auth v],
GE [auth C],
GF [auth E],
GL [auth d],
HE [auth C],
HG [auth T],
HM [auth k],
IE [auth C],
IK [auth c],
JK [auth c],
KC [auth B],
KK [auth c],
LC [auth B],
LG [auth V],
MC [auth B],
MH [auth a],
NC [auth B],
NH [auth a],
OC [auth B],
OG [auth V],
OH [auth a],
OK [auth c],
OM [auth o],
PG [auth V],
QC [auth B],
QG [auth V],
RH [auth a],
RM [auth o],
VK [auth d],
VL [auth h],
XI [auth b],
YF [auth L],
YI [auth b],
YM [auth u],
ZI [auth b],
ZM [auth v]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

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AD [auth B]
AM [auth i]
BD [auth B]
BF [auth D]
CD [auth B]
AD [auth B],
AM [auth i],
BD [auth B],
BF [auth D],
CD [auth B],
DD [auth B],
DE [auth C],
ED [auth B],
EG [auth O],
GJ [auth b],
GN [auth v],
HF [auth E],
HJ [auth b],
IJ [auth b],
IL [auth d],
JL [auth d],
KN [auth z],
LE [auth C],
PK [auth c],
QK [auth c],
QM [auth o],
RG [auth V],
RK [auth c],
SK [auth c],
SM [auth o],
TK [auth c],
TM [auth o],
UG [auth Y],
UM [auth o],
VM [auth o],
WH [auth a]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

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DH [auth a],
JB [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2 (Subject of Investigation/LOI)
Query on FE2

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AH [auth a],
OA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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BG [auth O]
JF [auth F]
KB [auth B]
KJ [auth c]
OL [auth f]
BG [auth O],
JF [auth F],
KB [auth B],
KJ [auth c],
OL [auth f],
PM [auth o],
ZH [auth b]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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BH [auth a],
CH [auth a],
PA [auth A],
QA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
DM [auth j],
RF [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL

Download Ideal Coordinates CCD File 
AF [auth D]
BJ [auth b]
BM [auth j]
CJ [auth b]
CM [auth j]
AF [auth D],
BJ [auth b],
BM [auth j],
CJ [auth b],
CM [auth j],
DB [auth A],
DF [auth E],
DJ [auth b],
EB [auth A],
EE [auth C],
EF [auth E],
EJ [auth b],
EM [auth k],
FB [auth A],
FD [auth C],
FJ [auth b],
FL [auth d],
GB [auth A],
HN [auth x],
IM [auth l],
IN [auth x],
JE [auth C],
JG [auth T],
JJ [auth c],
LK [auth c],
LL [auth e],
MF [auth H],
MK [auth c],
NE [auth D],
NF [auth I],
NK [auth c],
PC [auth B],
PF [auth I],
PH [auth a],
QF [auth I],
QH [auth a],
QL [auth h],
RC [auth B],
SC [auth B],
SG [auth Y],
SH [auth a],
SL [auth h],
TC [auth B],
TF [auth J],
TH [auth a],
UC [auth B],
UF [auth J],
VC [auth B],
VG [auth X],
WC [auth B],
WK [auth d],
WL [auth h],
WM [auth t],
XL [auth i],
YL [auth i],
ZE [auth D],
ZL [auth i]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HSK
Query on HSK
D,
W [auth d]
L-PEPTIDE LINKINGC6 H9 N3 O3HIS
FME
Query on FME
AA [auth i],
H [auth I]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.018α = 90
b = 229.579β = 90
c = 287.18γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMACrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

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