2AXT | pdb_00002axt

Crystal Structure of Photosystem II from Thermosynechococcus elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.286 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 4.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 720.87 kDa 
  • Atom Count: 48,254 
  • Modeled Residue Count: 5,286 
  • Deposited Residue Count: 5,546 
  • Unique protein chains: 18

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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Reference Sequence
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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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Reference Sequence
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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
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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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Reference Sequence
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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
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 L proteinCA [auth l],
K [auth L]
37Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence

Small Molecules

Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
FE [auth a],
SA [auth A]
OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-UHFFFAOYSA-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



Download:Ideal Coordinates CCD File
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
UNL

Query on UNL



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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 ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.286 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
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
  • Version 4.0: 2025-02-05
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary