1IZL

Crystal Structure of Photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Work: 0.530 
  • R-Value Observed: 0.530 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolution

Kamiya, N.Shen, J.-R.

(2003) Proc Natl Acad Sci U S A 100: 98-103

  • DOI: 10.1073/pnas.0135651100
  • Primary Citation of Related Structures:  
    1IZL

  • PubMed Abstract: 
  • Photosystem II (PSII) is a multisubunit membrane protein complex performing light-induced electron transfer and water-splitting reactions, leading to the formation of molecular oxygen. The first crystal structure of PSII from a thermophilic cyanobacterium Thermosynechococcus elongatus was reported recently [Zouni, A ...

    Photosystem II (PSII) is a multisubunit membrane protein complex performing light-induced electron transfer and water-splitting reactions, leading to the formation of molecular oxygen. The first crystal structure of PSII from a thermophilic cyanobacterium Thermosynechococcus elongatus was reported recently [Zouni, A., Witt, H. T., Kern, J., Fromme, P., Krauss, N., Saenger, W. & Orth, P. (2001) Nature 409, 739-743)] at 3.8-A resolution. To analyze the PSII structure in more detail, we have obtained the crystal structure of PSII from another thermophilic cyanobacterium, Thermosynechococcus vulcanus, at 3.7-A resolution. The present structure was built on the basis of the sequences of PSII large subunits D1, D2, CP47, and CP43; extrinsic 33- and 12-kDa proteins and cytochrome c550; and several low molecular mass subunits, among which the structure of the 12-kDa protein was not reported previously. This yielded much information concerning the molecular interactions within this large protein complex. We also show the arrangement of chlorophylls and cofactors, including two beta-carotenes recently identified in a region close to the reaction center, which provided important clues to the secondary electron transfer pathways around the reaction center. Furthermore, possible ligands for the Mn-cluster were determined. In particular, the C terminus of D1 polypeptide was shown to be connected to the Mn cluster directly. The structural information obtained here provides important insights into the mechanism of PSII reactions.


    Organizational Affiliation

    RIKEN Harima InstituteSPring-8, Kouto 1-1-1, Mikazuki-cho, Sayou-gun, Hyogo 679-5148, Japan. nkamiya@sp8sun.spring8.or.jp



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbAA,
O [auth J]
360Thermostichus vulcanusMutation(s): 0 
Gene Names: psbApsbA-1
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P51765 (Thermostichus vulcanus)
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UniProt GroupP51765
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbBB,
P [auth L]
472Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbBtlr1530
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbCC,
Q [auth M]
473Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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UniProt GroupQ8DIF8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbDD,
R [auth N]
352Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbD1tlr0455psbD2tlr1630
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbEE,
S [auth P]
83Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbEtsr1541
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbFF,
T [auth Q]
44Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbFtsr1542
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbGG,
U [auth R]
220Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbHH,
V [auth S]
33Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbII,
W [auth T]
26Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbKJ [auth K],
X [auth W]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbKtsl0176
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbOK [auth O],
Y
205Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbUL [auth U],
Z
97Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbVAA [auth 0],
M [auth V]
137Thermostichus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane Entity: Yes 
UniProt
Find proteins for P0A387 (Thermostichus vulcanus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II: Subunit PsbXBA [auth 1],
N [auth X]
25Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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AB [auth B],
AD [auth M],
BB [auth C],
BD [auth M],
CB [auth C],
AB [auth B],
AD [auth M],
BB [auth C],
BD [auth M],
CB [auth C],
CC [auth J],
CD [auth M],
DB [auth C],
DD [auth M],
EB [auth C],
EC [auth J],
ED [auth M],
FB [auth C],
FC [auth J],
FD [auth M],
GA [auth A],
GB [auth C],
GC [auth L],
GD [auth M],
HA [auth A],
HB [auth C],
HC [auth L],
IB [auth C],
IC [auth L],
ID [auth N],
JA [auth A],
JB [auth C],
JC [auth L],
JD [auth N],
KA [auth A],
KB [auth C],
KC [auth L],
KD [auth N],
LA [auth B],
LB [auth C],
LC [auth L],
MA [auth B],
MB [auth C],
MC [auth L],
MD [auth N],
NA [auth B],
NC [auth L],
OA [auth B],
OB [auth D],
OC [auth L],
PA [auth B],
PB [auth D],
PC [auth L],
PD [auth R],
QA [auth B],
QC [auth L],
QD [auth W],
RA [auth B],
RB [auth D],
RC [auth L],
SA [auth B],
SC [auth L],
TA [auth B],
TC [auth L],
UA [auth B],
UC [auth L],
VA [auth B],
VB [auth G],
VC [auth L],
WA [auth B],
WC [auth M],
XA [auth B],
XC [auth M],
YA [auth B],
YC [auth M],
ZA [auth B],
ZC [auth M]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

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DC [auth J],
IA [auth A],
LD [auth N],
QB [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
HEM
Query on HEM

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OD [auth P],
RD [auth 0],
UB [auth E],
XB [auth V]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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TB [auth D],
WB [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PLA
Query on PLA

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ND [auth N],
SB [auth D]
2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID
C13 H19 N2 O9 P
ZFKRUCNEKPIDBK-ZDUSSCGKSA-N
 Ligand Interaction
FE
Query on FE

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HD [auth N],
NB [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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AC [auth J],
BC [auth J],
CA [auth A],
DA [auth A],
EA [auth A],
AC [auth J],
BC [auth J],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
YB [auth J],
ZB [auth J]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Work: 0.530 
  • R-Value Observed: 0.530 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.377α = 90
b = 225.192β = 90
c = 308.672γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2012-11-28
    Changes: Other
  • Version 1.4: 2019-11-20
    Changes: Advisory, Database references, Derived calculations