1FE1

CRYSTAL STRUCTURE PHOTOSYSTEM II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of photosystem II from Synechococcus elongatus at 3.8 A resolution.

Zouni, A.Witt, H.T.Kern, J.Fromme, P.Krauss, N.Saenger, W.Orth, P.

(2001) Nature 409: 739-743

  • DOI: https://doi.org/10.1038/35055589
  • Primary Citation of Related Structures:  
    1FE1

  • PubMed Abstract: 

    Oxygenic photosynthesis is the principal energy converter on earth. It is driven by photosystems I and II, two large protein-cofactor complexes located in the thylakoid membrane and acting in series. In photosystem II, water is oxidized; this event provides the overall process with the necessary electrons and protons, and the atmosphere with oxygen. To date, structural information on the architecture of the complex has been provided by electron microscopy of intact, active photosystem II at 15-30 A resolution, and by electron crystallography on two-dimensional crystals of D1-D2-CP47 photosystem II fragments without water oxidizing activity at 8 A resolution. Here we describe the X-ray structure of photosystem II on the basis of crystals fully active in water oxidation. The structure shows how protein subunits and cofactors are spatially organized. The larger subunits are assigned and the locations and orientations of the cofactors are defined. We also provide new information on the position, size and shape of the manganese cluster, which catalyzes water oxidation.


  • Organizational Affiliation

    Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBA)
A, J
169Synechococcus elongatusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBD)
B, K
174Synechococcus elongatusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBC)
C, L
156Synechococcus elongatusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBB)
D, M
155Synechococcus elongatusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBE)
E, N
40Synechococcus elongatusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBF)
F, O
30Synechococcus elongatusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PHOTOSYSTEM II: SUBUNIT UNKNOWN)
G, P
312Synechococcus elongatusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBO)
H, Q
115Synechococcus elongatusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBV)
I, R
87Synechococcus elongatusMutation(s): 0 
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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AB [auth D]
BA [auth A]
BB [auth D]
BC [auth L]
BD [auth P]
AB [auth D],
BA [auth A],
BB [auth D],
BC [auth L],
BD [auth P],
CB [auth D],
CC [auth L],
DB [auth D],
DC [auth L],
EA [auth B],
EB [auth D],
EC [auth L],
FB [auth D],
FC [auth L],
GA [auth B],
GB [auth D],
GC [auth L],
HC [auth L],
IA [auth C],
IB [auth G],
IC [auth L],
JA [auth C],
JC [auth L],
KA [auth C],
KC [auth L],
LA [auth C],
LC [auth L],
MA [auth C],
MC [auth L],
NA [auth C],
NC [auth M],
OA [auth C],
OC [auth M],
PA [auth C],
PC [auth M],
QA [auth C],
QB [auth J],
QC [auth M],
RA [auth C],
RB [auth J],
RC [auth M],
SA [auth C],
SB [auth J],
SC [auth M],
TA [auth C],
TC [auth M],
UA [auth D],
UB [auth J],
UC [auth M],
VA [auth D],
VC [auth M],
WA [auth D],
WC [auth M],
X [auth A],
XA [auth D],
XB [auth K],
XC [auth M],
Y [auth A],
YA [auth D],
YC [auth M],
Z [auth A],
ZA [auth D],
ZB [auth K],
ZC [auth M]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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AA [auth A],
FA [auth B],
TB [auth J],
YB [auth K]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
HEM
Query on HEM

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AD [auth O],
DD [auth R],
HB [auth F],
KB [auth I]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PLA
Query on PLA

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AC [auth K],
HA [auth B]
2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID
C13 H19 N2 O9 P
ZFKRUCNEKPIDBK-ZDUSSCGKSA-N
TYR
Query on TYR

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DA [auth B],
PB [auth J],
W [auth A],
WB [auth K]
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
CD
Query on CD

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CD [auth Q],
JB [auth H]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
FE
Query on FE

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CA [auth B],
VB [auth K]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MN
Query on MN

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LB [auth J]
MB [auth J]
NB [auth J]
OB [auth J]
S [auth A]
LB [auth J],
MB [auth J],
NB [auth J],
OB [auth J],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.01α = 90
b = 226.72β = 90
c = 308.29γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
DMmodel building
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance