2AXT

Crystal Structure of Photosystem II from Thermosynechococcus elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

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This is version 3.0 of the entry. See complete history


Literature

Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II

Loll, B.Kern, J.Saenger, W.Zouni, A.Biesiadka, J.

(2005) Nature 438: 1040-1044

  • DOI: https://doi.org/10.1038/nature04224
  • Primary Citation of Related Structures:  
    2AXT

  • PubMed Abstract: 

    Oxygenic photosynthesis in plants, algae and cyanobacteria is initiated at photosystem II, a homodimeric multisubunit protein-cofactor complex embedded in the thylakoid membrane. Photosystem II captures sunlight and powers the unique photo-induced oxidation of water to atmospheric oxygen. Crystallographic investigations of cyanobacterial photosystem II have provided several medium-resolution structures (3.8 to 3.2 A) that explain the general arrangement of the protein matrix and cofactors, but do not give a full picture of the complex. Here we describe the most complete cyanobacterial photosystem II structure obtained so far, showing locations of and interactions between 20 protein subunits and 77 cofactors per monomer. Assignment of 11 beta-carotenes yields insights into electron and energy transfer and photo-protection mechanisms in the reaction centre and antenna subunits. The high number of 14 integrally bound lipids reflects the structural and functional importance of these molecules for flexibility within and assembly of photosystem II. A lipophilic pathway is proposed for the diffusion of secondary plastoquinone that transfers redox equivalents from photosystem II to the photosynthetic chain. The structure provides information about the Mn4Ca cluster, where oxidation of water takes place. Our study uncovers near-atomic details necessary to understand the processes that convert light to chemical energy.


  • Organizational Affiliation

    Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem Q(B) proteinA,
S [auth a]
344Thermosynechococcus vestitusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CP47 proteinB,
T [auth b]
510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
photosystem II CP43 proteinC,
U [auth c]
473Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
photosystem II reaction center D2 proteinD,
V [auth d]
352Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 alpha subunitE,
W [auth e]
84Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 beta subunitF,
X [auth f]
45Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center H proteinG [auth H],
Y [auth h]
66Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center I proteinH [auth I],
Z [auth i]
38Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center J proteinAA [auth j],
I [auth J]
40Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KBA [auth k],
J [auth K]
37Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center L proteinCA [auth l],
K [auth L]
37Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center M proteinDA [auth m],
L [auth M]
36Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideEA [auth o],
M [auth O]
247Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center T proteinFA [auth t],
N [auth T]
32Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinGA [auth u],
O [auth U]
104Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
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-550HA [auth v],
P [auth V]
137Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
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
Unassigned subunitsIA [auth x],
Q [auth X]
129Thermosynechococcus vestitusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center Z proteinJA [auth z],
R [auth Z]
62Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AD [auth C]
BD [auth C]
KG [auth c]
LG [auth c]
MD [auth H]
AD [auth C],
BD [auth C],
KG [auth c],
LG [auth c],
MD [auth H],
MG [auth c],
YG [auth h],
ZC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AB [auth B]
AE [auth a]
AG [auth c]
BB [auth B]
BG [auth c]
AB [auth B],
AE [auth a],
AG [auth c],
BB [auth B],
BG [auth c],
CB [auth B],
CG [auth c],
DB [auth B],
DD [auth D],
DE [auth a],
DG [auth c],
EB [auth B],
ED [auth D],
EG [auth c],
FB [auth B],
FG [auth c],
GB [auth B],
GG [auth c],
HB [auth B],
IB [auth B],
JB [auth B],
JC [auth C],
JE [auth b],
KB [auth B],
KC [auth C],
KE [auth b],
LA [auth A],
LB [auth B],
LC [auth C],
LE [auth b],
MA [auth A],
MB [auth B],
MC [auth C],
ME [auth b],
NA [auth A],
NB [auth B],
NC [auth C],
NE [auth b],
OC [auth C],
OE [auth b],
OG [auth d],
PC [auth C],
PE [auth b],
PG [auth d],
QA [auth A],
QC [auth C],
QE [auth b],
RC [auth C],
RE [auth b],
SC [auth C],
SE [auth b],
TC [auth C],
TE [auth b],
UC [auth C],
UE [auth b],
UF [auth c],
VC [auth C],
VE [auth b],
VF [auth c],
WE [auth b],
WF [auth c],
XE [auth b],
XF [auth c],
YA [auth B],
YD [auth a],
YE [auth b],
YF [auth c],
ZA [auth B],
ZD [auth a],
ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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BE [auth a],
CE [auth a],
OA [auth A],
PA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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EH [auth t]
QD [auth L]
SG [auth d]
VA [auth A]
XA [auth A]
EH [auth t],
QD [auth L],
SG [auth d],
VA [auth A],
XA [auth A],
XD [auth a]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LHG
Query on LHG

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HE [auth a],
UA [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
MGE
Query on MGE

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BH [auth l]
CF [auth b]
HD [auth D]
ID [auth D]
JD [auth D]
BH [auth l],
CF [auth b],
HD [auth D],
ID [auth D],
JD [auth D],
ND [auth I],
PD [auth L],
RB [auth B],
TG [auth d],
UG [auth d],
VG [auth d],
ZG [auth i]
(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
C38 H72 O10
FIJGNIAJTZSERN-DQQGJSMTSA-N
HEM
Query on HEM

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GH [auth v],
KD [auth F],
UD [auth V],
WG [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PQ9
Query on PQ9

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EE [auth a],
FD [auth D],
QG [auth d],
RA [auth A]
5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
C43 H64 O2
JXUCGUASMMLSBH-HOHOQCMASA-N
BCR
Query on BCR

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AF [auth b]
BF [auth b]
DH [auth t]
GD [auth D]
GE [auth a]
AF [auth b],
BF [auth b],
DH [auth t],
GD [auth D],
GE [auth a],
HG [auth c],
HH [auth x],
IG [auth c],
JG [auth c],
LD [auth H],
OB [auth B],
PB [auth B],
QB [auth B],
RG [auth d],
TA [auth A],
TD [auth T],
VD [auth X],
WC [auth C],
XC [auth C],
XG [auth h],
YC [auth C],
ZE [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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CH [auth m]
FH [auth t]
IE [auth a]
RD [auth M]
SD [auth T]
CH [auth m],
FH [auth t],
IE [auth a],
RD [auth M],
SD [auth T],
WA [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEC
Query on OEC

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FE [auth a],
SA [auth A]
OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-UHFFFAOYSA-N
UNK
Query on UNK

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AC [auth C]
BC [auth C]
CC [auth C]
DC [auth C]
DF [auth c]
AC [auth C],
BC [auth C],
CC [auth C],
DC [auth C],
DF [auth c],
EC [auth C],
EF [auth c],
FC [auth C],
FF [auth c],
GC [auth C],
GF [auth c],
HC [auth C],
HF [auth c],
IC [auth C],
IF [auth c],
JF [auth c],
KF [auth c],
LF [auth c],
MF [auth c],
NF [auth c],
OF [auth c],
PF [auth c],
QF [auth c],
RF [auth c],
SB [auth C],
SF [auth c],
TB [auth C],
TF [auth c],
UB [auth C],
VB [auth C],
WB [auth C],
XB [auth C],
YB [auth C],
ZB [auth C]
UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
BCT
Query on BCT

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CD [auth D],
NG [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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KA [auth A],
WD [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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AH [auth k],
OD [auth K]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.692α = 90
b = 225.403β = 90
c = 306.106γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 2.0: 2017-12-20
    Changes: Atomic model
  • Version 3.0: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary