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), 0.286 (DCC) 
  • R-Value Work: 
    0.269 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 
    0.269 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 742.08 kDa 
  • Atom Count: 50,266 
  • Modeled Residue Count: 5,280 
  • Deposited Residue Count: 5,494 
  • Unique protein chains: 20

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
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Reference Sequence
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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
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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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Reference Sequence
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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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Reference Sequence

Small Molecules

Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
AD [auth AC]
BD [auth AC]
GC [auth AB]
HH [auth BE]
LH [auth BH]
AD [auth AC],
BD [auth AC],
GC [auth AB],
HH [auth BE],
LH [auth BH],
ND [auth AE],
PG [auth BC],
QG [auth BC],
RD [auth AH],
RG [auth BC],
SE [auth BA],
XE [auth BB],
YA [auth AA],
ZC [auth AC]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AF [auth BB]
AG [auth BC]
BF [auth BB]
BG [auth BC]
CF [auth BB]
AF [auth BB],
AG [auth BC],
BF [auth BB],
BG [auth BC],
CF [auth BB],
CG [auth BC],
DF [auth BB],
DG [auth BC],
ED [auth AD],
EF [auth BB],
EG [auth BC],
FB [auth AB],
FF [auth BB],
FG [auth BC],
GB [auth AB],
GF [auth BB],
GG [auth BC],
HB [auth AB],
HD [auth AD],
HF [auth BB],
HG [auth BC],
IB [auth AB],
IF [auth BB],
IG [auth BC],
JB [auth AB],
JC [auth AC],
JF [auth BB],
JG [auth BC],
KB [auth AB],
KC [auth AC],
KF [auth BB],
KG [auth BC],
LB [auth AB],
LC [auth AC],
LE [auth BA],
LF [auth BB],
LG [auth BC],
MB [auth AB],
MC [auth AC],
ME [auth BA],
MF [auth BB],
NB [auth AB],
NC [auth AC],
NE [auth BA],
NF [auth BB],
OB [auth AB],
OC [auth AC],
OE [auth BA],
OF [auth BB],
PB [auth AB],
PC [auth AC],
PF [auth BB],
QB [auth AB],
QC [auth AC],
RA [auth AA],
RB [auth AB],
RC [auth AC],
SA [auth AA],
SB [auth AB],
SC [auth AC],
TA [auth AA],
TB [auth AB],
TC [auth AC],
UA [auth AA],
UB [auth AB],
UC [auth AC],
VC [auth AC],
WG [auth BD],
ZF [auth BC],
ZG [auth BD]
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]
AB [auth AA],
AC [auth AB],
DB [auth AA],
FC [auth AB],
HE [auth BA],
JH [auth BF],
PD [auth AF],
UE [auth BA],
UF [auth BB],
WE [auth BB]
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]
BB [auth AA],
CD [auth AC],
CH [auth BD],
DD [auth AC],
DH [auth BD],
EB [auth AA],
EH [auth BD],
GH [auth BE],
IE [auth BA],
KD [auth AD],
LD [auth AD],
MH [auth BI],
RH [auth BL],
SD [auth AI],
SG [auth BC],
TF [auth BB],
TG [auth BC],
TH [auth BM],
WD [auth AJ],
YB [auth AB],
ZB [auth AB],
ZD [auth AM]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
BH [auth BD]
CE [auth AT]
GE [auth AX]
JD [auth AD]
MG [auth BC]
BH [auth BD],
CE [auth AT],
GE [auth AX],
JD [auth AD],
MG [auth BC],
NG [auth BC],
OG [auth BC],
OH [auth BJ],
QF [auth BB],
QH [auth BK],
RE [auth BA],
RF [auth BB],
SF [auth BB],
VB [auth AB],
VD [auth AJ],
VH [auth BT],
WB [auth AB],
WC [auth AC],
XA [auth AA],
XB [auth AB],
XC [auth AC],
YC [auth AC],
YD [auth AK],
ZH [auth BX]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT


Download:Ideal Coordinates CCD File
AE [auth AM]
BC [auth AB]
CC [auth AB]
FH [auth BD]
HC [auth AB]
AE [auth AM],
BC [auth AB],
CC [auth AB],
FH [auth BD],
HC [auth AB],
IC [auth AB],
MD [auth AD],
NH [auth BI],
SH [auth BM],
TD [auth AI],
UD [auth AI],
UG [auth BC],
VF [auth BB],
WF [auth BB],
YE [auth BB],
ZE [auth BB]
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
DC [auth AB]
DE [auth AU]
EC [auth AB]
FE [auth AV]
XF [auth BB]
DC [auth AB],
DE [auth AU],
EC [auth AB],
FE [auth AV],
XF [auth BB],
XH [auth BV],
YF [auth BB],
YH [auth BV]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT

Query on BCT


Download:Ideal Coordinates CCD File
JE [auth BA],
PA [auth AA]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


Download:Ideal Coordinates CCD File
OA [auth AA],
VG [auth BD]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
BE [auth AO]
KH [auth BF]
PH [auth BK]
QD [auth AF]
UH [auth BO]
BE [auth AO],
KH [auth BF],
PH [auth BK],
QD [auth AF],
UH [auth BO],
XD [auth AK]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
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), 0.286 (DCC) 
  • R-Value Work:  0.269 (Depositor), 0.264 (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

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Ligand Structure Quality Assessment 


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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