4V82

Crystal structure of cyanobacterial Photosystem II in complex with terbutryn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.Biol.Chem. 286: 15964-15972

  • DOI: 10.1074/jbc.M110.215970
  • Primary Citation of Related Structures:  

  • 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 o ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem Q(B) protein 1
AA, BA
344Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbA1 (psbA-1)
EC: 1.10.3.9
Find proteins for P0A444 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A444
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II core light harvesting protein
AB, BB
510Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbB
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 protein
AC, BC
461Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbC
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIF8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
AD, BD
352Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbD1, psbD2
EC: 1.10.3.9
Find proteins for Q8CM25 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8CM25
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
AE, BE
84Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbE
Find proteins for Q8DIP0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIP0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
AF, BF
45Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbF
Find proteins for Q8DIN9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
AH, BH
66Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbH
Find proteins for Q8DJ43 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJ43
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
AI, BI
38Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbI
Find proteins for Q8DJZ6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJZ6
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
AJ, BJ
40Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbJ
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P59087
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
AK, BK
37Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbK
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1K9
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
AL, BL
37Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbL
Find proteins for Q8DIN8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
AM, BM
36Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbM
Find proteins for Q8DHA7 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DHA7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
AO, BO
247Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbO
Find proteins for P0A431 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A431
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
AT, BT
32Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbT
Find proteins for Q8DIQ0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ0
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
AU, BU
104Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbU
Find proteins for Q9F1L5 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1L5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
AV, BV
137Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbV
Find proteins for P0A386 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A386
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein ycf12
Ay, By
46Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ycf12
Find proteins for Q8DJI1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJI1
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center X protein
AX, BX
41Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbX
Find proteins for Q9F1R6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1R6
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM II PSBX PROTEIN
AY, BY
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
AZ, BZ
62Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbZ
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DHJ2
Small Molecules
Ligands 17 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

Download SDF File 
Download CCD File 
AA, AB, AF, BA, BB, BF
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
CLA
Query on CLA

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AA, AB, AC, AD, BA, BB, BC, BD
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

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Download CCD File 
AD, BD
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
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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AA, BA
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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AF, AK, AO, BF, BK, BO
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DGD
Query on DGD

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AA, AB, AC, AE, AH, BA, BB, BC, BE, BH
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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AA, AB, AC, AD, AI, AJ, AM, BA, BB, BC, BD, BE, BI, BL, BM
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCT
Query on BCT

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Download CCD File 
AA, BA
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
AF, AV, BF, BV
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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AA, AB, AC, AD, AJ, AK, AT, AX, BA, BB, BC, BD, BJ, BK, BT, BX
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

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AD, BD
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
FE2
Query on FE2

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AA, BD
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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AB, AD, AI, AM, BB, BC, BD, BI, BM
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
AB, AU, AV, BB, BV
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MST
Query on MST

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Download CCD File 
AA, BA
2-T-BUTYLAMINO-4-ETHYLAMINO-6-METHYLTHIO-S-TRIAZINE
C10 H19 N5 S
IROINLKCQGIITA-UHFFFAOYSA-N
 Ligand Interaction
OEC
Query on OEC

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AA, BA
OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-MBOUAFFSAW
 Ligand Interaction
LHG
Query on LHG

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Download CCD File 
AA, BA
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
AY, BY
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.269 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 128.080α = 90.00
b = 225.370β = 90.00
c = 305.680γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other