5B66

Crystal structure analysis of Photosystem II complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report



Literature

Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II

Tanaka, A.Fukushima, Y.Kamiya, N.

(2017) J Am Chem Soc 139: 1718-1721

  • DOI: 10.1021/jacs.6b09666
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The oxygen-evolving complex (OEC) forms the heart of photosystem II (PSII) in photosynthesis. The crystal structure of PSII from Thermosynechococcus vulcanus has been reported at a resolution of 1.9 Å and at an averaged X-ray dose of 0.43 MGy. The OE ...

    The oxygen-evolving complex (OEC) forms the heart of photosystem II (PSII) in photosynthesis. The crystal structure of PSII from Thermosynechococcus vulcanus has been reported at a resolution of 1.9 Å and at an averaged X-ray dose of 0.43 MGy. The OEC structure is suggested to be partially reduced to Mn(II) by EXAFS and DFT computational studies. Recently, the "radiation-damage-free" structures have been published at 1.95 Å resolution using XFEL, but reports continued to appear that the OEC is reduced to the S 0 -state of the Kok cycle. To elucidate much more precise structure of the OEC, in this study two structures were determined at extremely low X-ray doses of 0.03 and 0.12 MGy using conventional synchrotron radiation source. The results indicated that the X-ray reduction effects on the OEC were very small in the low dose region below 0.12 MGy, that is, a threshold existed for the OEC structural changes caused by X-ray exposure. The OEC structures of the two identical monomers in the crystal were clearly different under the threshold of the radiation dose, although the surrounding polypeptide frameworks of PSII were the same. The assumption that the OECs in the crystal were in the dark-stable S 1 -state of the Kok cycle should be re-evaluated.


    Organizational Affiliation

    The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D, d
342Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Find proteins for D0VWR8 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR8

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
83Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbE
Find proteins for P12238 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12238

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbK
Find proteins for P19054 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19054

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbL
Find proteins for P12241 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12241

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
32Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbT
Find proteins for P12313 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12313

Find similar proteins by: Sequence  |  Structure

Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbV
Find proteins for P0A387 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P0A387

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y, y
30Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: ycf12psbY
Find proteins for D0VWR3 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR3

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbZ
Find proteins for D0VWR5 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR5

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein D1
A, a
344Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbApsbA-1
EC: 1.10.3.9
Find proteins for P51765 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P51765

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
M, m
36Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbM
Find proteins for P12312 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12312

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
244Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbO
Find proteins for D0VWR2 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR2

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
104Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbU
Find proteins for P56152 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P56152

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein X
X, x
40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbX
Find proteins for D0VWR4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR4

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center protein
B, b
505Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbB
Find proteins for D0VWR1 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR1

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 reaction center protein
C, c
455Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbC
Find proteins for D0VWR7 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR7

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
44Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbF
Find proteins for P12239 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12239

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
65Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbH
Find proteins for P19052 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19052

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
38Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbI
Find proteins for P12240 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12240

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbJ
Find proteins for Q7DGD4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  Q7DGD4
Small Molecules
Ligands 21 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download CCD File 
C, D, H, c, d, h
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA
Query on CLA

Download CCD File 
A, B, C, D, a, b, c, d
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

Download CCD File 
A, D, a
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD
Query on SQD

Download CCD File 
A, F, a, b, f, l
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
LMG
Query on LMG

Download CCD File 
A, B, C, J, a, b, c, j
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
PL9
Query on PL9

Download CCD File 
A, D, a, d
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
 Ligand Interaction
LHG
Query on LHG

Download CCD File 
D, E, L, d, l
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEC
Query on HEC

Download CCD File 
V, v
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

Download CCD File 
E, e
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
RRX
Query on RRX

Download CCD File 
H, x
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
 Ligand Interaction
BCR
Query on BCR

Download CCD File 
A, B, C, D, K, T, a, b, c, d, j, k, t
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

Download CCD File 
B, E, I, J, M, T, Z, a, b, c, f, m, z
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEX
Query on OEX

Download CCD File 
A, a
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
HTG
Query on HTG

Download CCD File 
B, C, D, O, V, b, c, d, u, v
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A, B, C, D, F, H, O, U, V, b, c, d, h, i, j, o, u, v
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download CCD File 
A, a
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
A, a
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
B, O, V, b, c, o
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, a
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
J, j
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download CCD File 
A, B, C, D, E, H, I, J, L, M, T, U, X, Z, a, b, c, d, e, h, i, j, t, x, z
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
T,tL-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.465α = 90
b = 228.176β = 90
c = 286.422γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grants-in-Aid for Scientific ResearchJapanH24227002

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references
  • Version 2.0: 2019-10-09
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary