4V82 | pdb_00004v82

Crystal structure of cyanobacterial Photosystem II in complex with terbutryn

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.299 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.269 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.269 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DGDClick on this verticalbar to view detailsBest fitted CLAClick on this verticalbar to view detailsBest fitted PHOClick on this verticalbar to view detailsBest fitted SQDClick on this verticalbar to view detailsBest fitted LMGClick on this verticalbar to view detailsBest fitted PL9Click on this verticalbar to view detailsBest fitted LHGClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view detailsBest fitted BCRClick on this verticalbar to view detailsBest fitted LMTClick on this verticalbar to view detailsBest fitted MSTClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history. 


Literature

Structural basis of cyanobacterial photosystem II Inhibition by the herbicide terbutryn

Broser, M., Glockner, C., Gabdulkhakov, A., Guskov, A., Buchta, J., Kern, J., Muh, F., Dau, H., Saenger, W., Zouni, A.

(2011) J Biological Chem 286: 15964-15972

  • DOI: https://doi.org/10.1074/jbc.M110.215970
  • Primary Citation of Related Structures:  
    4V82

  • PubMed Abstract: 

    Herbicides that target photosystem II (PSII) compete with the native electron acceptor plastoquinone for binding at the Q(B) site in the D1 subunit and thus block the electron transfer from Q(A) to Q(B). Here, we present the first crystal structure of PSII with a bound herbicide at a resolution of 3.2 Å. The crystallized PSII core complexes were isolated from the thermophilic cyanobacterium Thermosynechococcus elongatus. The used herbicide terbutryn is found to bind via at least two hydrogen bonds to the Q(B) site similar to photosynthetic reaction centers in anoxygenic purple bacteria. Herbicide binding to PSII is also discussed regarding the influence on the redox potential of Q(A), which is known to affect photoinhibition. We further identified a second and novel chloride position close to the water-oxidizing complex and in the vicinity of the chloride ion reported earlier (Guskov, A., Kern, J., Gabdulkhakov, A., Broser, M., Zouni, A., and Saenger, W. (2009) Nat. Struct. Mol. Biol. 16, 334-342). This discovery is discussed in the context of proton transfer to the lumen.

    • Organizational Affiliation: 

    Institut für Chemie/Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A [auth AA],
U [auth BA]		344Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB [auth AB],
V [auth BB]		510Thermosynechococcus vestitus BP-1Mutation(s): 0 
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 proteinC [auth AC],
W [auth BC]		461Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD [auth AD],
X [auth BD]		352Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE [auth AE],
Y [auth BE]		84Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF [auth AF],
Z [auth BF]		45Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth BH],
G [auth AH]		66Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth BI],
H [auth AI]		38Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth BJ],
I [auth AJ]		40Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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 KDA [auth BK],
J [auth AK]		37Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth BL],
K [auth AL]		37Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth BM],
L [auth AM]		36Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth BO],
M [auth AO]		247Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth BT],
N [auth AT]		32Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth BU],
O [auth AU]		104Thermosynechococcus vestitus BP-1Mutation(s): 0 
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-550JA [auth BV],
P [auth AV]		137Thermosynechococcus vestitus BP-1Mutation(s): 0 
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 protein ycf12KA [auth By],
Q [auth Ay]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinLA [auth BX],
R [auth AX]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II PSBX PROTEINMA [auth BY],
S [auth AY]		28Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZNA [auth BZ],
T [auth AZ]		62Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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AD [auth AC]
BD [auth AC]
GC [auth AB]
HH [auth BE]
LH [auth BH]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA
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AF [auth BB]
AG [auth BC]
BF [auth BB]
BG [auth BC]
CF [auth BB]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO
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FD [auth AD],
GD [auth AD],
XG [auth BD],
YG [auth BD]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD
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AB [auth AA]
AC [auth AB]
DB [auth AA]
FC [auth AB]
HE [auth BA]
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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BB [auth AA]
CD [auth AC]
CH [auth BD]
DD [auth AC]
DH [auth BD]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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AH [auth BD],
ID [auth AD]		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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CB [auth AA],
TE [auth BA],
VE [auth BA],
ZA [auth AA]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM
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EE [auth AV],
IH [auth BF],
OD [auth AF],
WH [auth BV]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR
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BH [auth BD]
CE [auth AT]
GE [auth AX]
JD [auth AD]
MG [auth BC]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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AE [auth AM]
BC [auth AB]
CC [auth AB]
FH [auth BD]
HC [auth AB]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEC
Query on OEC
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QE [auth BA],
WA [auth AA]		OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-UHFFFAOYSA-N
MST
Query on MST
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PE [auth BA],
VA [auth AA]		2-T-BUTYLAMINO-4-ETHYLAMINO-6-METHYLTHIO-S-TRIAZINE
C10 H19 N5 S
IROINLKCQGIITA-UHFFFAOYSA-N
DMS
Query on DMS
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DC [auth AB]
DE [auth AU]
EC [auth AB]
FE [auth AV]
XF [auth BB]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT
Query on BCT
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JE [auth BA],
PA [auth AA]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
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OA [auth AA],
VG [auth BD]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA
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BE [auth AO]
KH [auth BF]
PH [auth BK]
QD [auth AF]
UH [auth BO]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
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KE [auth BA],
QA [auth AA]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.299 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.269 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.269 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.08α = 90
b = 225.37β = 90
c = 305.68γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
CNSrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DGDClick on this verticalbar to view detailsBest fitted CLAClick on this verticalbar to view detailsBest fitted PHOClick on this verticalbar to view detailsBest fitted SQDClick on this verticalbar to view detailsBest fitted LMGClick on this verticalbar to view detailsBest fitted PL9Click on this verticalbar to view detailsBest fitted LHGClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view detailsBest fitted BCRClick on this verticalbar to view detailsBest fitted LMTClick on this verticalbar to view detailsBest fitted MSTClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 2.0: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
  • Version 2.1: 2024-11-20
    Changes: Structure summary