PDBsum entry 3bz2

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protein ligands metals Protein-protein interface(s) links
Electron transport PDB id
Protein chains
335 a.a. *
490 a.a. *
447 a.a. *
340 a.a. *
82 a.a. *
35 a.a. *
65 a.a. *
35 a.a. *
34 a.a. *
37 a.a. *
37 a.a. *
34 a.a. *
243 a.a. *
32 a.a. *
97 a.a. *
137 a.a. *
28 a.a. *
37 a.a. *
28 a.a. *
62 a.a. *
CLA ×35
PHO ×2
HEM ×2
PL9 ×3
BCR ×12
DGD ×7
LHG ×2
SQD ×5
LMT ×7
* Residue conservation analysis
PDB id:
Name: Electron transport
Title: Crystal structure of cyanobacterial photosystem ii (part 2 o file contains second monomer of psii dimer
Structure: Photosystem q(b) protein. Chain: a. Fragment: unp residues 1-344. Synonym: 32 kda thylakoid membrane protein, photosystem ii d1. Photosystem ii core light harvesting protein. Chain: b. Photosystem ii cp43 protein. Chain: c.
Source: Thermosynechococcus elongatus. Organism_taxid: 197221. Strain: bp-1. Strain: bp-1
2.90Å     R-factor:   0.249     R-free:   0.292
Authors: A.Guskov,A.Gabdulkhakov,J.Kern,M.Broser,A.Zouni,W.Saenger
Key ref:
A.Guskov et al. (2009). Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride. Nat Struct Biol, 16, 334-342. PubMed id: 19219048 DOI: 10.1038/nsmb.1559
17-Jan-08     Release date:   20-Jan-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0A444  (PSBA1_THEEB) -  Photosystem Q(B) protein 1
360 a.a.
335 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DIQ1  (Q8DIQ1_THEEB) -  Photosystem II core light harvesting protein
510 a.a.
490 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DIF8  (Q8DIF8_THEEB) -  Photosystem II CP43 protein
461 a.a.
447 a.a.
Protein chain
Pfam   ArchSchema ?
Q8CM25  (PSBD_THEEB) -  Photosystem II D2 protein
352 a.a.
340 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DIP0  (PSBE_THEEB) -  Cytochrome b559 subunit alpha
84 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DIN9  (PSBF_THEEB) -  Cytochrome b559 subunit beta
45 a.a.
35 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DJ43  (PSBH_THEEB) -  Photosystem II reaction center protein H
66 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DJZ6  (PSBI_THEEB) -  Photosystem II reaction center protein I
38 a.a.
35 a.a.
Protein chain
Pfam   ArchSchema ?
P59087  (PSBJ_THEEB) -  Photosystem II reaction center protein J
40 a.a.
34 a.a.
Protein chain
Pfam   ArchSchema ?
Q9F1K9  (PSBK_THEEB) -  Photosystem II reaction center protein K
46 a.a.
37 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DIN8  (PSBL_THEEB) -  Photosystem II reaction center protein L
37 a.a.
37 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DHA7  (PSBM_THEEB) -  Photosystem II reaction center protein M
36 a.a.
34 a.a.
Protein chain
Pfam   ArchSchema ?
P0A431  (PSBO_THEEB) -  Photosystem II manganese-stabilizing polypeptide
272 a.a.
243 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DIQ0  (PSBT_THEEB) -  Photosystem II reaction center protein T
32 a.a.
32 a.a.
Protein chain
Pfam   ArchSchema ?
Q9F1L5  (PSBU_THEEB) -  Photosystem II 12 kDa extrinsic protein
134 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
P0A386  (CY550_THEEB) -  Cytochrome c-550
163 a.a.
137 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DJI1  (YCF12_THEEB) -  Photosystem II reaction center protein Ycf12
46 a.a.
28 a.a.
Protein chain
Pfam   ArchSchema ?
Q9F1R6  (PSBX_THEEB) -  Photosystem II reaction center X protein
41 a.a.
37 a.a.
Protein chain
No UniProt id for this chain
Struc: 28 a.a.
Protein chain
Pfam   ArchSchema ?
Q8DHJ2  (PSBZ_THEEB) -  Photosystem II reaction center protein Z
62 a.a.
62 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, D: E.C.  - Photosystem Ii.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 H2O + 2 plastoquinone + 4 light = O2 + 2 plastoquinol
2 × H(2)O
2 × plastoquinone
Bound ligand (Het Group name = PL9)
matches with 42.86% similarity
+ 4 × light
= O(2)
+ 2 × plastoquinol
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   12 terms 
  Biological process     oxidation-reduction process   10 terms 
  Biochemical function     electron carrier activity     10 terms  


DOI no: 10.1038/nsmb.1559 Nat Struct Biol 16:334-342 (2009)
PubMed id: 19219048  
Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride.
A.Guskov, J.Kern, A.Gabdulkhakov, M.Broser, A.Zouni, W.Saenger.
Photosystem II (PSII) is a large homodimeric protein-cofactor complex located in the photosynthetic thylakoid membrane that acts as light-driven water:plastoquinone oxidoreductase. The crystal structure of PSII from Thermosynechococcus elongatus at 2.9-A resolution allowed the unambiguous assignment of all 20 protein subunits and complete modeling of all 35 chlorophyll a molecules and 12 carotenoid molecules, 25 integral lipids and 1 chloride ion per monomer. The presence of a third plastoquinone Q(C) and a second plastoquinone-transfer channel, which were not observed before, suggests mechanisms for plastoquinol-plastoquinone exchange, and we calculated other possible water or dioxygen and proton channels. Putative oxygen positions obtained from a Xenon derivative indicate a role for lipids in oxygen diffusion to the cytoplasmic side of PSII. The chloride position suggests a role in proton-transfer reactions because it is bound through a putative water molecule to the Mn(4)Ca cluster at a distance of 6.5 A and is close to two possible proton channels.
  Selected figure(s)  
Figure 3.
(a) Schematic view of the PQ-PQH[2] exchange cavity and the two entry and exit portals connecting the Q[B] and Q[C] sites to the PQ pool in the thylakoid membrane. Approximate dimensions are given in angstroms; Q[B] and Q[C] are colored cyan and yellow, respectively, the Q[B] site is highlighted in pink, and the three lipids forming the cork (the head groups for PG22, SQDG4 and MGDG18 are shown as red, green and white squares) nearly closing the cavity toward the cytoplasm are indicated. (b) Calculated channels (I and II, gray) for PQ-PQH[2] transfer between the PQ pool and the Q[B] and Q[C] sites, viewed from the cytoplasmic side. Shown are the PQs in the Q[B] site (light blue) and Q[C] site (yellow), non-heme Fe^2+ (blue sphere), Car15 (orange), Chl37 (green), SQDG4 (gray), cyt b-559 heme (dark blue) and the surrounding proteins (pink). Car[D2], Chl[D2] and MGDG7 are not shown. (c) Possible mechanisms for the PQ-PQH[2] exchange between the Q[B] site of PSII and the PQ pool in the thylakoid membrane, viewed from the cytoplasm. Channels I and II open toward the PQ pool. PQ is shown with a red and PQH[2] with a blue head group. The Q[B] site is highlighted pink, the Q[C] site in green and labeled; the yellow patch indicates a hydrophobic region formed by the fatty acids of MGDG7, MGDG18 and the phytol chain of Chl[D2]. Small arrows symbolize movements of PQ molecules. See text for explanations concerning the alternating, wriggling and single-channel mechanisms.
Figure 4.
(a) Position of Cl^- (green sphere) located in the native electron density (blue, contoured at 1.2 level) close to the Mn[4]Ca cluster (red and orange spheres; Mn1 is partially hidden behind Mn2). The coordinating amino acids are from D1 (yellow) except for D2-Lys317 (orange). (b) Enlarged view of the neighborhood of Cl^- showing coordinating amino acids and electron density (blue, contoured at 1.2 level) for a putative water molecule (purple sphere) located between Mn4 and Cl^-. Distances are given in angstroms.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 334-342) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21469224 A.R.Jaszewski, S.Petrie, R.J.Pace, and R.Stranger (2011).
Toward the Assignment of the Manganese Oxidation Pattern in the Water-Oxidizing Complex of Photosystem II: A Time-Dependent DFT Study of XANES Energies.
  Chemistry, 17, 5699-5713.  
20512415 A.Williamson, B.Conlan, W.Hillier, and T.Wydrzynski (2011).
The evolution of Photosystem II: insights into the past and future.
  Photosynth Res, 107, 71-86.  
21487931 C.Pagliano, F.Chimirri, G.Saracco, F.Marsano, and J.Barber (2011).
One-step isolation and biochemical characterization of a highly active plant PSII monomeric core.
  Photosynth Res, 108, 33-46.  
21548696 D.Abramavicius, and S.Mukamel (2011).
Exciton dynamics in chromophore aggregates with correlated environment fluctuations.
  J Chem Phys, 134, 174504.  
21145779 E.R.Moellering, and C.Benning (2011).
Galactoglycerolipid metabolism under stress: a time for remodeling.
  Trends Plant Sci, 16, 98.  
21336416 E.Romero, I.H.van Stokkum, J.P.Dekker, and R.van Grondelle (2011).
Ultrafast carotenoid band shifts correlated with ChlZ excited states in the photosystem II reaction center: are the carotenoids involved in energy transfer?
  Phys Chem Chem Phys, 13, 5573-5575.  
21249156 G.Rea, M.Lambreva, F.Polticelli, I.Bertalan, A.Antonacci, S.Pastorelli, M.Damasso, U.Johanningmeier, and M.T.Giardi (2011).
Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure.
  PLoS One, 6, e16216.  
  21288250 I.Vass (2011).
Role of charge recombination processes in photodamage and photoprotection of the photosystem II complex.
  Physiol Plant, 142, 6.  
21265891 J.G.García-Cerdán, L.Kovács, T.Tóth, S.Kereïche, E.Aseeva, E.J.Boekema, F.Mamedov, C.Funk, and W.P.Schröder (2011).
The PsbW protein stabilizes the supramolecular organization of photosystem II in higher plants.
  Plant J, 65, 368-381.  
21438681 M.F.Hohmann-Marriott, and R.E.Blankenship (2011).
Evolution of photosynthesis.
  Annu Rev Plant Biol, 62, 515-548.  
21359392 M.M.Najafpour (2011).
A soluble form of nano-sized colloidal manganese(IV) oxide as an efficient catalyst for water oxidation.
  Dalton Trans, 40, 3805-3807.  
21344591 M.Sener, J.Strümpfer, J.Hsin, D.Chandler, S.Scheuring, C.N.Hunter, and K.Schulten (2011).
Förster energy transfer theory as reflected in the structures of photosynthetic light-harvesting systems.
  Chemphyschem, 12, 518-531.  
21118826 M.Watanabe, H.Kubota, H.Wada, R.Narikawa, and M.Ikeuchi (2011).
Novel supercomplex organization of photosystem I in Anabaena and Cyanophora paradoxa.
  Plant Cell Physiol, 52, 162-168.  
21539776 S.Caffarri, K.Broess, R.Croce, and H.van Amerongen (2011).
Excitation Energy Transfer and Trapping in Higher Plant Photosystem II Complexes with Different Antenna Sizes.
  Biophys J, 100, 2094-2103.  
21327234 S.Nayak, H.P.Nayek, S.Dehnen, A.K.Powell, and J.Reedijk (2011).
Trigonal propeller-shaped [Mn(III)3M(II)Na] complexes (M = Mn, Ca): structural and functional models for the dioxygen evolving centre of PSII.
  Dalton Trans, 40, 2699-2702.  
21585320 T.Y.Fufina, L.G.Vasilieva, R.A.Khatypov, and V.A.Shuvalov (2011).
Properties of Rhodobacter sphaeroides Photosynthetic Reaction Center with Double Amino Acid Substitution I(L177)H+H(M182)L.
  Biochemistry (Mosc), 76, 450-454.  
21499260 Y.Umena, K.Kawakami, J.R.Shen, and N.Kamiya (2011).
Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å.
  Nature, 473, 55-60.
PDB codes: 3arc 3wu2
19923216 A.Amunts, H.Toporik, A.Borovikova, and N.Nelson (2010).
Structure determination and improved model of plant photosystem I.
  J Biol Chem, 285, 3478-3486.
PDB codes: 2wsc 2wse 2wsf 3lw5
20352642 A.Guskov, A.Gabdulkhakov, M.Broser, C.Glöckner, J.Hellmich, J.Kern, J.Frank, F.Müh, W.Saenger, and A.Zouni (2010).
Recent progress in the crystallographic studies of photosystem II.
  Chemphyschem, 11, 1160-1171.  
20054625 A.Jajoo, S.Mathur, P.Mehta, M.Yashioka, M.Yoshoika, S.I.Allakhverdiev, and Y.Yamamoto (2010).
Study on the effects of chloride depletion on photosystem II using different chloride depletion methods.
  J Bioenerg Biomembr, 42, 47-53.  
20845333 B.Thangaraj, C.M.Ryan, P.Souda, K.Krause, K.F.Faull, A.P.Weber, P.Fromme, and J.P.Whitelegge (2010).
Data-directed top-down Fourier-transform mass spectrometry of a large integral membrane protein complex: photosystem II from Galdieria sulphuraria.
  Proteomics, 10, 3644-3656.  
20007972 C.H.Hung, H.J.Hwang, Y.H.Chen, Y.F.Chiu, S.C.Ke, R.L.Burnap, and H.A.Chu (2010).
Spectroscopic and functional characterizations of cyanobacterium Synechocystis PCC 6803 mutants on and near the heme axial ligand of cytochrome b559 in photosystem II.
  J Biol Chem, 285, 5653-5663.  
20707578 D.Abramavicius, and S.Mukamel (2010).
Quantum oscillatory exciton migration in photosynthetic reaction centers.
  J Chem Phys, 133, 064510.  
21073225 D.Abramavicius, and S.Mukamel (2010).
Energy-transfer and charge-separation pathways in the reaction center of photosystem II revealed by coherent two-dimensional optical spectroscopy.
  J Chem Phys, 133, 184501.  
20192195 H.C.Fry, A.Lehmann, J.G.Saven, W.F.DeGrado, and M.J.Therien (2010).
Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore.
  J Am Chem Soc, 132, 3997-4005.  
20521115 H.N.Su, B.B.Xie, X.Y.Zhang, B.C.Zhou, and Y.Z.Zhang (2010).
The supramolecular architecture, function, and regulation of thylakoid membranes in red algae: an overview.
  Photosynth Res, 106, 73-87.  
20544016 I.Ohad, H.Raanan, N.Keren, D.Tchernov, and A.Kaplan (2010).
Light-induced changes within photosystem II protects Microcoleus sp. in biological desert sand crusts against excess light.
  PLoS One, 5, e11000.  
  19960065 J.H.Su, and J.Messinger (2010).
Is Mn-Bound Substrate Water Protonated in the S(2) State of Photosystem II?
  Appl Magn Reson, 37, 123-136.  
20194360 M.Iwai, T.Suzuki, A.Kamiyama, I.Sakurai, N.Dohmae, Y.Inoue, and M.Ikeuchi (2010).
The PsbK subunit is required for the stable assembly and stability of other small subunits in the PSII complex in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.
  Plant Cell Physiol, 51, 554-560.  
20231245 O.Sozer, J.Komenda, B.Ughy, I.Domonkos, H.Laczkó-Dobos, P.Malec, Z.Gombos, and M.Kis (2010).
Involvement of carotenoids in the synthesis and assembly of protein subunits of photosynthetic reaction centers of Synechocystis sp. PCC 6803.
  Plant Cell Physiol, 51, 823-835.  
20338950 P.J.Nixon, F.Michoux, J.Yu, M.Boehm, and J.Komenda (2010).
Recent advances in understanding the assembly and repair of photosystem II.
  Ann Bot, 106, 1.  
20391456 P.Liebisch, and H.Dau (2010).
Linear dichroism in the XANES of partially oriented samples: theory and application to the photosynthetic manganese complex.
  Chemphyschem, 11, 1236-1247.  
20607375 R.K.Sinha, A.Tiwari, and P.Pospísil (2010).
Water-splitting manganese complex controls light-induced redox changes of cytochrome b559 in photosystem II.
  J Bioenerg Biomembr, 42, 337-344.  
20375107 R.Nagao, T.Suzuki, A.Okumura, A.Niikura, M.Iwai, N.Dohmae, T.Tomo, J.R.Shen, M.Ikeuchi, and I.Enami (2010).
Topological analysis of the extrinsic PsbO, PsbP and PsbQ proteins in a green algal PSII complex by cross-linking with a water-soluble carbodiimide.
  Plant Cell Physiol, 51, 718-727.  
20142495 S.I.Allakhverdiev, T.Tomo, Y.Shimada, H.Kindo, R.Nagao, V.V.Klimov, and M.Mimuro (2010).
Redox potential of pheophytin a in photosystem II of two cyanobacteria having the different special pair chlorophylls.
  Proc Natl Acad Sci U S A, 107, 3924-3929.  
20391525 S.Kessen, C.Teutloff, J.Kern, A.Zouni, and R.Bittl (2010).
High-field 2H-Mims-ENDOR spectroscopy on PSII single crystals: hydrogen bonding of YD*.
  Chemphyschem, 11, 1275-1282.  
20457933 S.Larom, F.Salama, G.Schuster, and N.Adir (2010).
Engineering of an alternative electron transfer path in photosystem II.
  Proc Natl Acad Sci U S A, 107, 9650-9655.  
20967896 S.Petrie, R.Stranger, and R.J.Pace (2010).
Hydration preferences for Mn4Ca cluster models of photosystem II: location of potential substrate-water binding sites.
  Chemistry, 16, 14026-14042.  
20164644 S.Westenhoff, E.Nazarenko, E.Malmerberg, J.Davidsson, G.Katona, and R.Neutze (2010).
Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches.
  Acta Crystallogr A, 66, 207-219.  
20139160 T.H.Chang, F.L.Hsieh, T.P.Ko, K.H.Teng, P.H.Liang, and A.H.Wang (2010).
Structure of a heterotetrameric geranyl pyrophosphate synthase from mint (Mentha piperita) reveals intersubunit regulation.
  Plant Cell, 22, 454-467.
PDB codes: 3kra 3krc 3krf 3kro 3krp
20394099 T.Renger, and E.Schlodder (2010).
Primary photophysical processes in photosystem II: bridging the gap between crystal structure and optical spectra.
  Chemphyschem, 11, 1141-1153.  
20547590 T.Takami, M.Shibata, Y.Kobayashi, and T.Shikanai (2010).
De novo biosynthesis of fatty acids plays critical roles in the response of the photosynthetic machinery to low temperature in Arabidopsis.
  Plant Cell Physiol, 51, 1265-1275.  
19639145 C.Teutloff, S.Pudollek, S.Keßen, M.Broser, A.Zouni, and R.Bittl (2009).
Electronic structure of the tyrosine D radical and the water-splitting complex from pulsed ENDOR spectroscopy on photosystem II single crystals.
  Phys Chem Chem Phys, 11, 6715-6726.  
19639153 D.A.Pantazis, M.Orio, T.Petrenko, S.Zein, W.Lubitz, J.Messinger, and F.Neese (2009).
Structure of the oxygen-evolving complex of photosystem II: information on the S(2) state through quantum chemical calculation of its magnetic properties.
  Phys Chem Chem Phys, 11, 6788-6798.  
19586025 D.L.Jenson, and B.A.Barry (2009).
Proton-coupled electron transfer in photosystem II: proton inventory of a redox active tyrosine.
  J Am Chem Soc, 131, 10567-10573.  
19783985 D.Pogoryelov, O.Yildiz, J.D.Faraldo-Gómez, and T.Meier (2009).
High-resolution structure of the rotor ring of a proton-dependent ATP synthase.
  Nat Struct Mol Biol, 16, 1068-1073.
PDB code: 2wie
19617353 M.Khatoon, K.Inagawa, P.Pospísil, A.Yamashita, M.Yoshioka, B.Lundin, J.Horie, N.Morita, A.Jajoo, Y.Yamamoto, and Y.Yamamoto (2009).
Quality control of photosystem II: Thylakoid unstacking is necessary to avoid further damage to the D1 protein and to facilitate D1 degradation under light stress in spinach thylakoids.
  J Biol Chem, 284, 25343-25352.  
19568951 M.Komura, and S.Itoh (2009).
Fluorescence measurement by a streak camera in a single-photon-counting mode.
  Photosynth Res, 101, 119-133.  
20025311 M.Reppert, V.Naibo, and R.Jankowiak (2009).
Analytical formulas for low-fluence non-line-narrowed hole-burned spectra in an excitonically coupled dimer.
  J Chem Phys, 131, 234104.  
19667103 M.Watanabe, M.Iwai, R.Narikawa, and M.Ikeuchi (2009).
Is the photosystem II complex a monomer or a dimer?
  Plant Cell Physiol, 50, 1674-1680.  
19468713 N.Mizusawa, S.Sakata, I.Sakurai, N.Sato, and H.Wada (2009).
Involvement of digalactosyldiacylglycerol in cellular thermotolerance in Synechocystis sp. PCC 6803.
  Arch Microbiol, 191, 595-601.  
19696744 S.Caffarri, R.Kouril, S.Kereïche, E.J.Boekema, and R.Croce (2009).
Functional architecture of higher plant photosystem II supercomplexes.
  EMBO J, 28, 3052-3063.  
19633919 T.S.Kuntzleman, and A.Haddy (2009).
Fluoride inhibition of photosystem II and the effect of removal of the PsbQ subunit.
  Photosynth Res, 102, 7.  
19552399 Y.Gao, K.E.Shinopoulos, C.A.Tracewell, A.L.Focsan, G.W.Brudvig, and L.D.Kispert (2009).
Formation of carotenoid neutral radicals in photosystem II.
  J Phys Chem B, 113, 9901-9908.  
19805064 Y.Kato, M.Sugiura, A.Oda, and T.Watanabe (2009).
Spectroelectrochemical determination of the redox potential of pheophytin a, the primary electron acceptor in photosystem II.
  Proc Natl Acad Sci U S A, 106, 17365-17370.  
  20848333 , (2000).
Treatment news bulletin.
  Curr Treat Options Neurol, 2, 1-4.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.