7YQ7

Crystal structure of photosystem II expressing psbA3 gene only

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

Starting Model: experimental
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Literature

Crystal structures of photosystem II from a cyanobacterium expressing psbA 2 in comparison to psbA 3 reveal differences in the D1 subunit.

Nakajima, Y., Ugai-Amo, N., Tone, N., Nakagawa, A., Iwai, M., Ikeuchi, M., Sugiura, M., Suga, M., Shen, J.R.

(2022) J Biol Chem 298: 102668-102668

  • DOI: https://doi.org/10.1016/j.jbc.2022.102668
  • Primary Citation of Related Structures:  
    7YQ2, 7YQ7

  • PubMed Abstract: 

    Three psbA genes (psbA 1 , psbA 2 , and psbA 3 ) encoding the D1 subunit of photosystem II (PSII) are present in the thermophilic cyanobacterium Thermosynechococcus elongatus and are expressed differently in response to changes in the growth environment. To clarify the functional differences of the D1 protein expressed from these psbA genes, PSII dimers from two strains, each expressing only one psbA gene (psbA 2 or psbA 3 ), were crystallized, and we analyzed their structures at resolutions comparable to previously studied PsbA1-PSII. Our results showed that the hydrogen bond between pheophytin/D1 (Pheo D1 ) and D1-130 became stronger in PsbA2- and PsbA3-PSII due to change of Gln to Glu, which partially explains the increase in the redox potential of Pheo D1 observed in PsbA3. In PsbA2, one hydrogen bond was lost in Pheo D1 due to the change of D1-Y147F, which may explain the decrease in stability of Pheo D1 in PsbA2. Two water molecules in the Cl-1 channel were lost in PsbA2 due to the change of D1-P173M, leading to the narrowing of the channel, which may explain the lower efficiency of the S-state transition beyond S 2 in PsbA2-PSII. In PsbA3-PSII, a hydrogen bond between D1-Ser270 and a sulfoquinovosyl-diacylglycerol molecule near Q B disappeared due to the change of D1-Ser270 in PsbA1 and PsbA2 to D1-Ala270. This may result in an easier exchange of bound Q B with free plastoquinone, hence an enhancement of oxygen evolution in PsbA3-PSII due to its high Q B exchange efficiency. These results provide a structural basis for further functional examination of the three PsbA variants.

    • Organizational Affiliation: 

    Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1 3A,
T [auth a]		360Thermosynechococcus vestitus BP-1Mutation(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,
U [auth b]		510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]		461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]		352Thermosynechococcus vestitus BP-1Mutation(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]		84Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]		45Thermosynechococcus vestitus BP-1Mutation(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]		66Thermosynechococcus vestitus BP-1Mutation(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]		38Thermosynechococcus vestitus BP-1Mutation(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]		40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]		46Thermosynechococcus vestitus BP-1Mutation(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]		37Thermosynechococcus vestitus BP-1Mutation(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]		36Thermosynechococcus vestitus BP-1Mutation(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]		272Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]		32Thermosynechococcus vestitus BP-1Mutation(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]		134Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]		163Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinJA [auth x],
Q [auth X]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth y],
R [auth Y]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]		62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YMA [auth R]41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 22 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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BL [auth c]
CL [auth c]
DL [auth c]
MM [auth d]
TF [auth H]
BL [auth c],
CL [auth c],
DL [auth c],
MM [auth d],
TF [auth H],
UD [auth C],
VD [auth C],
WD [auth C],
WM [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA
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AC [auth B]
AI [auth a]
AJ [auth b]
BC [auth B]
BI [auth a]
AC [auth B],
AI [auth a],
AJ [auth b],
BC [auth B],
BI [auth a],
BJ [auth b],
BM [auth d],
CC [auth B],
CI [auth a],
CJ [auth b],
CM [auth d],
DC [auth B],
DJ [auth b],
EI [auth a],
EJ [auth b],
FD [auth C],
FJ [auth b],
GD [auth C],
GJ [auth b],
HD [auth C],
HJ [auth b],
ID [auth C],
IJ [auth b],
JD [auth C],
JJ [auth b],
KD [auth C],
KJ [auth b],
LD [auth C],
LJ [auth b],
MD [auth C],
MK [auth c],
ND [auth C],
NK [auth c],
OB [auth B],
OD [auth C],
OK [auth c],
PB [auth B],
PD [auth C],
PK [auth c],
QB [auth B],
QD [auth C],
QK [auth c],
RA [auth A],
RB [auth B],
RD [auth C],
RE [auth D],
RK [auth c],
SA [auth A],
SB [auth B],
SK [auth c],
TB [auth B],
TK [auth c],
UB [auth B],
UK [auth c],
VA [auth A],
VB [auth B],
VE [auth D],
VK [auth c],
WB [auth B],
WE [auth D],
WI [auth b],
WK [auth c],
XB [auth B],
XI [auth b],
XK [auth c],
YB [auth B],
YI [auth b],
YK [auth c],
ZB [auth B],
ZI [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO (Subject of Investigation/LOI)
Query on PHO
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DI [auth a],
TA [auth A],
UA [auth A],
XL [auth d]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD (Subject of Investigation/LOI)
Query on SQD
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BB [auth A]
GI [auth a]
HC [auth B]
NF [auth F]
SH [auth a]
BB [auth A],
GI [auth a],
HC [auth B],
NF [auth F],
SH [auth a],
SI [auth b],
UM [auth f],
XA [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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CN [auth i]
DF [auth D]
EL [auth c]
FL [auth c]
IC [auth B]
CN [auth i],
DF [auth D],
EL [auth c],
FL [auth c],
IC [auth B],
IM [auth d],
JE [auth C],
JO [auth z],
OH [auth Z],
PJ [auth b],
XD [auth C],
YA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9
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EM [auth d],
II [auth a],
YE [auth D],
ZA [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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AF [auth D]
BF [auth D]
CF [auth D]
FM [auth d]
GM [auth d]
AF [auth D],
BF [auth D],
CF [auth D],
FM [auth d],
GM [auth d],
HI [auth a],
HM [auth d],
IG [auth L],
JF [auth E],
ON [auth l]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC
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AH [auth V],
CO [auth v]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM
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OF [auth F],
RM [auth e]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX
Query on RRX
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SF [auth H],
VM [auth h]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR
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AL [auth c]
DM [auth d]
EC [auth B]
FC [auth B]
FI [auth a]
AL [auth c],
DM [auth d],
EC [auth B],
FC [auth B],
FI [auth a],
GC [auth B],
GG [auth K],
HG [auth K],
KN [auth k],
LN [auth k],
MJ [auth b],
NJ [auth b],
OJ [auth b],
SD [auth C],
TD [auth C],
VG [auth T],
WA [auth A],
XE [auth D],
XN [auth t],
ZK [auth c]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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CG [auth J]
HN [auth j]
IB [auth A]
JC [auth B]
JG [auth M]
CG [auth J],
HN [auth j],
IB [auth A],
JC [auth B],
JG [auth M],
KG [auth M],
MI [auth a],
PF [auth F],
QJ [auth b],
QN [auth m],
RJ [auth b],
RN [auth m],
SE [auth D],
TH [auth a],
TM [auth f],
UJ [auth b],
XC [auth B],
ZE [auth D]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX
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NA [auth A],
VH [auth a]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG
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AM [auth d]
BH [auth V]
GL [auth c]
HL [auth c]
KC [auth B]
AM [auth d],
BH [auth V],
GL [auth c],
HL [auth c],
KC [auth B],
LC [auth B],
NG [auth O],
OC [auth B],
PC [auth B],
QF [auth H],
SJ [auth b],
SN [auth o],
TI [auth b],
TJ [auth b],
UI [auth b],
YD [auth C],
ZD [auth C],
ZN [auth u]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL
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BE [auth C]
DK [auth b]
EB [auth A]
EK [auth b]
EO [auth v]
BE [auth C],
DK [auth b],
EB [auth A],
EK [auth b],
EO [auth v],
GH [auth V],
HB [auth A],
HF [auth D],
KI [auth a],
LM [auth d],
OG [auth O]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS
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AD [auth B]
AO [auth u]
BD [auth B]
BN [auth h]
BO [auth u]
AD [auth B],
AO [auth u],
BD [auth B],
BN [auth h],
BO [auth u],
CD [auth B],
CH [auth V],
DD [auth C],
DO [auth v],
FO [auth v],
GK [auth b],
GO [auth v],
HH [auth V],
HK [auth b],
IF [auth D],
IH [auth V],
IK [auth b],
JH [auth V],
JK [auth b],
KB [auth A],
KE [auth C],
KH [auth V],
LB [auth A],
LE [auth C],
ME [auth C],
MF [auth E],
MG [auth O],
ML [auth c],
NE [auth C],
NI [auth a],
NL [auth c],
NM [auth d],
OE [auth C],
OI [auth a],
OL [auth c],
OM [auth d],
PE [auth C],
PG [auth O],
PI [auth a],
PL [auth c],
PM [auth d],
QE [auth C],
QG [auth O],
QI [auth a],
QL [auth c],
RC [auth B],
RG [auth O],
RI [auth a],
RL [auth c],
SC [auth B],
SG [auth O],
SL [auth c],
SM [auth e],
TC [auth B],
TG [auth O],
TL [auth c],
UG [auth O],
UH [auth a],
UL [auth c],
UN [auth o],
VL [auth c],
VN [auth o],
WJ [auth b],
WL [auth c],
WN [auth o],
XG [auth T],
XJ [auth b],
YC [auth B],
YG [auth T],
YJ [auth b],
ZC [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT
Query on BCT
Download Ideal Coordinates CCD File 
JB [auth A],
UE [auth D],
YL [auth d],
ZH [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
Download Ideal Coordinates CCD File 
OA [auth A],
WH [auth a]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
LG [auth O],
LK [auth c],
NB [auth B],
TN [auth o],
VI [auth b]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
PA [auth A],
QA [auth A],
XH [auth a],
YH [auth a]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
BG [auth J],
GN [auth j]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL
Download Ideal Coordinates CCD File 
AB [auth A]
AE [auth C]
AG [auth I]
AK [auth b]
AN [auth h]
AB [auth A],
AE [auth C],
AG [auth I],
AK [auth b],
AN [auth h],
BK [auth b],
CB [auth A],
CE [auth C],
CK [auth b],
DB [auth A],
DE [auth C],
DG [auth J],
DH [auth V],
DN [auth i],
ED [auth C],
EE [auth C],
EF [auth D],
EG [auth J],
EH [auth V],
EN [auth i],
FB [auth A],
FE [auth C],
FF [auth D],
FG [auth J],
FH [auth V],
FK [auth b],
FN [auth i],
GB [auth A],
GE [auth C],
GF [auth D],
HE [auth C],
HO [auth x],
IE [auth C],
IL [auth c],
IN [auth j],
IO [auth y],
JI [auth a],
JL [auth c],
JM [auth d],
JN [auth k],
KF [auth E],
KK [auth c],
KL [auth c],
KM [auth d],
KO [auth z],
LF [auth E],
LH [auth X],
LI [auth a],
LL [auth c],
MB [auth B],
MC [auth B],
MH [auth X],
MN [auth k],
NC [auth B],
NH [auth Y],
NN [auth l],
PH [auth Z],
PN [auth m],
QC [auth B],
QH [auth Z],
QM [auth e],
RF [auth H],
RH [auth Z],
TE [auth D],
UC [auth B],
UF [auth H],
VC [auth B],
VF [auth I],
VJ [auth b],
WC [auth B],
WF [auth I],
WG [auth T],
XF [auth I],
XM [auth h],
YF [auth I],
YM [auth h],
YN [auth t],
ZF [auth I],
ZG [auth U],
ZJ [auth b],
ZL [auth d],
ZM [auth h]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
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: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.804α = 90
b = 228.456β = 90
c = 286.852γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20H03226

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary