4PJ0

Structure of T.elongatus Photosystem II, rows of dimers crystal packing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Native-like Photosystem II Superstructure at 2.44 angstrom Resolution through Detergent Extraction from the Protein Crystal.

Hellmich, J.Bommer, M.Burkhardt, A.Ibrahim, M.Kern, J.Meents, A.Muh, F.Dobbek, H.Zouni, A.

(2014) Structure 22: 1607-1615

  • DOI: 10.1016/j.str.2014.09.007
  • Primary Citation of Related Structures:  
    4PJ0

  • PubMed Abstract: 
  • Photosystem II (PSII) catalyzes a key step in photosynthesis, the oxidation of water to oxygen. Excellent structural models exist for the dimeric PSII core complex of cyanobacteria, but higher order physiological assemblies readily dissociate when so ...

    Photosystem II (PSII) catalyzes a key step in photosynthesis, the oxidation of water to oxygen. Excellent structural models exist for the dimeric PSII core complex of cyanobacteria, but higher order physiological assemblies readily dissociate when solubilized from the native thylakoid membrane with detergent. Here, we describe the crystallization of PSII from Thermosynechococcus elongatus with a postcrystallization treatment involving extraction of the detergent C12E8. This resulted in a transition from Type II to Type I-like membrane protein crystals and improved diffraction to 2.44 Å resolution. The obtained PSII packing in precise rows, interconnected by specific pairs of galactolipids and a loop in the PsbO subunit specific to cyanobacteria, is superimposable with previous electron microscopy images of the thylakoid membrane. The study provides a detailed model of such a superstructure and its organization of light-harvesting pigments with possible implications for the understanding of their efficient use of solar energy.


    Organizational Affiliation

    Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10095 Berlin, Germany. Electronic address: athina.zouni@hu-berlin.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1Aa344Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbA1psbA-1tlr1843
EC: 1.10.3.9
Find proteins for P0A444 (Thermosynechococcus elongatus (strain BP-1))
Explore P0A444 
Go to UniProtKB:  P0A444
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CP47 proteinBb510Thermosynechococcus elongatusMutation(s): 0 
EC: 1.10.3.9
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DIQ1 
Go to UniProtKB:  Q8DIQ1
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 proteinCc461Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
EC: 1.10.3.9
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DIF8 
Go to UniProtKB:  Q8DIF8
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinDd352Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbD1tlr0455psbD2tlr1630
EC: 1.10.3.9
Find proteins for Q8CM25 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8CM25 
Go to UniProtKB:  Q8CM25
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaEe84Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbEtsr1541
EC: 1.10.3.9
Find proteins for Q8DIP0 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DIP0 
Go to UniProtKB:  Q8DIP0
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaFf45Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbFtsr1542
EC: 1.10.3.9
Find proteins for Q8DIN9 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DIN9 
Go to UniProtKB:  Q8DIN9
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HHh66Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbHtsl1386
EC: 1.10.3.9
Find proteins for Q8DJ43 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DJ43 
Go to UniProtKB:  Q8DJ43
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IIi38Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbItsr1074
EC: 1.10.3.9
Find proteins for Q8DJZ6 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DJZ6 
Go to UniProtKB:  Q8DJZ6
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JJj40Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbJtsr1544
EC: 1.10.3.9
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1))
Explore P59087 
Go to UniProtKB:  P59087
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KKk46Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbKtsl0176
EC: 1.10.3.9
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1))
Explore Q9F1K9 
Go to UniProtKB:  Q9F1K9
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LLl37Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbLtsr1543
EC: 1.10.3.9
Find proteins for Q8DIN8 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DIN8 
Go to UniProtKB:  Q8DIN8
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein MMm36Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbMtsl2052
EC: 1.10.3.9
Find proteins for Q8DHA7 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DHA7 
Go to UniProtKB:  Q8DHA7
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideOo272Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbOtll0444
EC: 1.10.3.9
Find proteins for P0A431 (Thermosynechococcus elongatus (strain BP-1))
Explore P0A431 
Go to UniProtKB:  P0A431
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TTt32Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbTtsr1531
EC: 1.10.3.9
Find proteins for Q8DIQ0 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DIQ0 
Go to UniProtKB:  Q8DIQ0
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinUu134Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbUtll2409
EC: 1.10.3.9
Find proteins for Q9F1L5 (Thermosynechococcus elongatus (strain BP-1))
Explore Q9F1L5 
Go to UniProtKB:  Q9F1L5
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550Vv163Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbVtll1285
EC: 1.10.3.9
Find proteins for P0A386 (Thermosynechococcus elongatus (strain BP-1))
Explore P0A386 
Go to UniProtKB:  P0A386
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12Yy46Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: ycf12tsr1242
EC: 1.10.3.9
Find proteins for Q8DJI1 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DJI1 
Go to UniProtKB:  Q8DJI1
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZZz62Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbZtsr1967
EC: 1.10.3.9
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DHJ2 
Go to UniProtKB:  Q8DHJ2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein YRr41Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbYtsl0836
EC: 1.10.3.9
Find proteins for Q8DKM3 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DKM3 
Go to UniProtKB:  Q8DKM3
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinXx41Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbXtsr2013
EC: 1.10.3.9
Find proteins for Q9F1R6 (Thermosynechococcus elongatus (strain BP-1))
Explore Q9F1R6 
Go to UniProtKB:  Q9F1R6
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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

Download CCD File 
A, F, L, a, f
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, D, a, b, c, d
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 
A, D, E, L, a, d, l
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM
Query on HEM

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

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

Download CCD File 
A, a
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, O, U, V, a, d, o, u
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BCT
Query on BCT

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

Download CCD File 
A, a
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Download CCD File 
B, C, D, I, J, M, T, X, b, c, d, i, j, k, m, t, x
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.447α = 90
b = 218.889β = 90
c = 302.202γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Structure summary
  • Version 1.2: 2014-12-24
    Changes: Database references