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PDBsum entry 2o01

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protein ligands Protein-protein interface(s) links
Photosynthesis PDB id
2o01
Jmol
Contents
Protein chains
728 a.a. *
732 a.a. *
80 a.a. *
138 a.a. *
62 a.a. *
154 a.a. *
95 a.a. *
75 a.a. *
30 a.a. *
42 a.a. *
37 a.a. *
164 a.a. *
85 a.a. *
175 a.a. *
166 a.a. *
115 a.a. *
165 a.a. *
Ligands
CLA ×168
SF4 ×3
PQN ×2
BCR ×5
* Residue conservation analysis
PDB id:
2o01
Name: Photosynthesis
Title: The structure of a plant photosystem i supercomplex at 3.4 a resolution
Structure: Photosystem i p700 chlorophyll a apoprotein a1. Chain: a. Synonym: psaa, psi-a. Photosystem i p700 chlorophyll a apoprotein a2. Chain: b. Synonym: psab, psi-b. Photosystem i iron-sulfur center. Chain: c. Synonym: photosystem i subunit vii, 9 kda polypeptide, psi-
Source: Pisum sativum. Pea. Organism_taxid: 3888. Strain: alaska. Spinacia oleracea. Spinach. Organism_taxid: 3562. Arabidopsis thaliana. Thale cress.
Resolution:
3.40Å     R-factor:   0.351     R-free:   0.409
Authors: A.Amunts,O.Drory,N.Nelson
Key ref:
A.Amunts et al. (2007). The structure of a plant photosystem I supercomplex at 3.4 A resolution. Nature, 447, 58-63. PubMed id: 17476261 DOI: 10.1038/nature05687
Date:
27-Nov-06     Release date:   08-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05310  (PSAA_PEA) -  Photosystem I P700 chlorophyll a apoprotein A1
Seq:
Struc:
 
Seq:
Struc:
758 a.a.
728 a.a.*
Protein chain
Pfam   ArchSchema ?
P05311  (PSAB_PEA) -  Photosystem I P700 chlorophyll a apoprotein A2
Seq:
Struc:
 
Seq:
Struc:
734 a.a.
732 a.a.*
Protein chain
Pfam   ArchSchema ?
P10793  (PSAC_PEA) -  Photosystem I iron-sulfur center
Seq:
Struc:
81 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P12353  (PSAD_SPIOL) -  Photosystem I reaction center subunit II, chloroplastic
Seq:
Struc:
212 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
Q9S831  (PSAE1_ARATH) -  Photosystem I reaction center subunit IV A, chloroplastic
Seq:
Struc:
143 a.a.
62 a.a.
Protein chain
Pfam   ArchSchema ?
P12355  (PSAF_SPIOL) -  Photosystem I reaction center subunit III, chloroplastic
Seq:
Struc:
231 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P12357  (PSAG_SPIOL) -  Photosystem I reaction center subunit V, chloroplastic
Seq:
Struc:
167 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P22179  (PSAH_SPIOL) -  Photosystem I reaction center subunit VI, chloroplastic
Seq:
Struc:
144 a.a.
75 a.a.
Protein chain
Pfam   ArchSchema ?
P17227  (PSAI_PEA) -  Photosystem I reaction center subunit VIII
Seq:
Struc:
40 a.a.
30 a.a.
Protein chain
Pfam   ArchSchema ?
P17230  (PSAJ_SPIOL) -  Photosystem I reaction center subunit IX
Seq:
Struc:
44 a.a.
42 a.a.
Protein chain
No UniProt id for this chain
Struc: 37 a.a.
Protein chain
Pfam   ArchSchema ?
Q41385  (PSAL_SPIOL) -  Photosystem I reaction center subunit XI, chloroplastic
Seq:
Struc:
216 a.a.
164 a.a.
Protein chain
Pfam   ArchSchema ?
Q84U30  (Q84U30_PHAVU) -  Photosystem I-N subunit
Seq:
Struc:
170 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
Q01667  (CAB6_ARATH) -  Chlorophyll a-b binding protein 6, chloroplastic
Seq:
Struc:
241 a.a.
175 a.a.
Protein chain
Pfam   ArchSchema ?
Q41038  (Q41038_PEA) -  Type II chlorophyll a/b binding protein from photosystem I
Seq:
Struc:
269 a.a.
166 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9SY97  (Q9SY97_ARATH) -  PSI type III chlorophyll a/b-binding protein
Seq:
Struc:
273 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
Q9SQL2  (CB24_PEA) -  Chlorophyll a-b binding protein P4, chloroplastic
Seq:
Struc:
252 a.a.
165 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.1.97.1.12  - Photosystem I.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   9 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     electron carrier activity     8 terms  

 

 
DOI no: 10.1038/nature05687 Nature 447:58-63 (2007)
PubMed id: 17476261  
 
 
The structure of a plant photosystem I supercomplex at 3.4 A resolution.
A.Amunts, O.Drory, N.Nelson.
 
  ABSTRACT  
 
All higher organisms on Earth receive energy directly or indirectly from oxygenic photosynthesis performed by plants, green algae and cyanobacteria. Photosystem I (PSI) is a supercomplex of a reaction centre and light-harvesting complexes. It generates the most negative redox potential in nature, and thus largely determines the global amount of enthalpy in living systems. We report the structure of plant PSI at 3.4 A resolution, revealing 17 protein subunits. PsaN was identified in the luminal side of the supercomplex, and most of the amino acids in the reaction centre were traced. The crystal structure of PSI provides a picture at near atomic detail of 11 out of 12 protein subunits of the reaction centre. At this level, 168 chlorophylls (65 assigned with orientations for Q(x) and Q(y) transition dipole moments), 2 phylloquinones, 3 Fe(4)S(4) clusters and 5 carotenoids are described. This structural information extends the understanding of the most efficient nano-photochemical machine in nature.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: The structural model of plant photosystem I at 3.4 Å resolution. View from the stroma of the structure of plant PSI. Novel structural elements that are not present in the previous model are shown as red ribbon structures. Chlorophylls with detected phytyl side chains, revealing the orientation of the Q[x] and Q[y] transition dipole moments, are yellow. The rest of the reaction centre chlorophylls are cyan, gap chlorophylls are blue and chlorophylls of LHCI are green. The positions of PsaG, H, K, L and N, as well as the various LHCI monomers, are indicated. Each individual subunit is coloured differently.
Figure 3.
Figure 3: The position of PsaN in relation to Lhca2 and Lhca3, and the unique fold of Lhca3. a, The 2F[o]F[c] (1 ) electron density map covering PsaN, and the structure of the Lhca2–Lhca3 heterodimer. Cyan, Lhca2; magenta, Lhca3; green, chlorophylls; yellow, magnesium atoms. b, Left panel, superposition of LHCII (magenta) on Lhca2 (green); right panel, superposition of LHCII (magenta) on Lhca3 (green).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 447, 58-63) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21548696 D.Abramavicius, and S.Mukamel (2011).
Exciton dynamics in chromophore aggregates with correlated environment fluctuations.
  J Chem Phys, 134, 174504.  
21083539 E.Wientjes, and R.Croce (2011).
The light-harvesting complexes of higher-plant Photosystem I: Lhca1/4 and Lhca2/3 form two red-emitting heterodimers.
  Biochem J, 433, 477-485.  
21274629 J.Liu, M.Yin, M.Wang, X.Zhang, B.Ge, S.Liu, J.Lu, and Z.Cui (2011).
A novel membrane based process to isolate photosystem-I membrane complex from spinach.
  Photosynth Res, 107, 187-193.  
20831593 J.Nickelsen, B.Rengstl, A.Stengel, M.Schottkowski, J.Soll, and E.Ankele (2011).
Biogenesis of the cyanobacterial thylakoid membrane system--an update.
  FEMS Microbiol Lett, 315, 1-5.  
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.  
21077900 X.Qin, W.Wang, K.Wang, Y.Xin, and T.Kuang (2011).
Isolation and characteristics of the PSI-LHCI-LHCII supercomplex under high light.
  Photochem Photobiol, 87, 143-150.  
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
20422003 B.Ge, F.Yang, D.Yu, S.Liu, and H.Xu (2010).
Designer amphiphilic short peptides enhance thermal stability of isolated photosystem-I.
  PLoS One, 5, e10233.  
20197046 B.van Oort, M.Alberts, S.de Bianchi, L.Dall'Osto, R.Bassi, G.Trinkunas, R.Croce, and H.van Amerongen (2010).
Effect of antenna-depletion in Photosystem II on excitation energy transfer in Arabidopsis thaliana.
  Biophys J, 98, 922-931.  
20596891 J.A.Neilson, and D.G.Durnford (2010).
Structural and functional diversification of the light-harvesting complexes in photosynthetic eukaryotes.
  Photosynth Res, 106, 57-71.  
  20495604 J.Niklas, O.Gopta, B.Epel, W.Lubitz, and M.L.Antonkine (2010).
Investigation of the Stationary and Transient A(1) Radical in Trp --> Phe Mutants of Photosystem I.
  Appl Magn Reson, 38, 187-203.  
19826804 K.McLuskey, A.W.Roszak, Y.Zhu, and N.W.Isaacs (2010).
Crystal structures of all-alpha type membrane proteins.
  Eur Biophys J, 39, 723-755.  
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
20142514 M.G.Müller, C.Slavov, R.Luthra, K.E.Redding, and A.R.Holzwarth (2010).
Independent initiation of primary electron transfer in the two branches of the photosystem I reaction center.
  Proc Natl Acad Sci U S A, 107, 4123-4128.  
20183922 R.Subramanyam, C.Jolley, B.Thangaraj, S.Nellaepalli, A.N.Webber, and P.Fromme (2010).
Structural and functional changes of PSI-LHCI supercomplexes of Chlamydomonas reinhardtii cells grown under high salt conditions.
  Planta, 231, 913-922.  
20405215 S.P.Romberger, and J.H.Golbeck (2010).
The bound iron-sulfur clusters of type-I homodimeric reaction centers.
  Photosynth Res, 104, 333-346.  
19446520 A.Amunts, and N.Nelson (2009).
Plant photosystem I design in the light of evolution.
  Structure, 17, 637-650.  
19037743 A.V.Ruban, and M.P.Johnson (2009).
Dynamics of higher plant photosystem cross-section associated with state transitions.
  Photosynth Res, 99, 173-183.  
19351124 D.Abramavicius, and S.Mukamel (2009).
Exciton delocalization and transport in photosystem I of cyanobacteria Synechococcus elongates: simulation study of coherent two-dimensional optical signals.
  J Phys Chem B, 113, 6097-6108.  
19139095 E.Wientjes, G.T.Oostergetel, S.Jansson, E.J.Boekema, and R.Croce (2009).
The role of lhca complexes in the supramolecular organization of higher plant photosystem I.
  J Biol Chem, 284, 7803-7810.  
19966409 J.Sanchez-Weatherby, M.W.Bowler, J.Huet, A.Gobbo, F.Felisaz, B.Lavault, R.Moya, J.Kadlec, R.B.Ravelli, and F.Cipriani (2009).
Improving diffraction by humidity control: a novel device compatible with X-ray beamlines.
  Acta Crystallogr D Biol Crystallogr, 65, 1237-1246.
PDB codes: 2w6e 2w6f 2w6g 2w6h 2w6i 2w6j
19125349 L.O.Björn, G.C.Papageorgiou, R.E.Blankenship, and Govindjee (2009).
A viewpoint: Why chlorophyll a?
  Photosynth Res, 99, 85-98.  
19129188 M.Ballottari, M.Mozzo, R.Croce, T.Morosinotto, and R.Bassi (2009).
Occupancy and functional architecture of the pigment binding sites of photosystem II antenna complex Lhcb5.
  J Biol Chem, 284, 8103-8113.  
19337668 M.H.Oh, R.B.Safarova, Y.J.Eu, I.S.Zulfugarov, J.H.Kim, H.J.Hwang, C.B.Lee, and C.H.Lee (2009).
Loss of peripheral polypeptides in the stromal side of photosystem I by light-chilling in cucumber leaves.
  Photochem Photobiol Sci, 8, 535-541.  
19568951 M.Komura, and S.Itoh (2009).
Fluorescence measurement by a streak camera in a single-photon-counting mode.
  Photosynth Res, 101, 119-133.  
19144643 R.Tokutsu, M.Iwai, and J.Minagawa (2009).
CP29, a Monomeric Light-harvesting Complex II Protein, Is Essential for State Transitions in Chlamydomonas reinhardtii.
  J Biol Chem, 284, 7777-7782.  
19277364 S.Silvi, E.C.Constable, C.E.Housecroft, J.E.Beves, E.L.Dunphy, M.Tomasulo, F.M.Raymo, and A.Credi (2009).
Photochemical switching of luminescence and singlet oxygen generation by chemical signal communication.
  Chem Commun (Camb), (), 1484-1486.  
19667102 T.Onishi, and Y.Takahashi (2009).
Effects of site-directed mutations in the chloroplast-encoded Ycf4 gene on PSI complex assembly in the green alga Chlamydomonas reinhardtii.
  Plant Cell Physiol, 50, 1750-1760.  
18931256 B.van Oort, A.Amunts, J.W.Borst, A.van Hoek, N.Nelson, H.van Amerongen, and R.Croce (2008).
Picosecond fluorescence of intact and dissolved PSI-LHCI crystals.
  Biophys J, 95, 5851-5861.  
18465006 C.C.Chu, and D.M.Bassani (2008).
Challenges and opportunities for photochemists on the verge of solar energy conversion.
  Photochem Photobiol Sci, 7, 521-530.  
18425141 C.M.Zhang, C.Liu, S.Slater, and Y.M.Hou (2008).
Aminoacylation of tRNA with phosphoserine for synthesis of cysteinyl-tRNA(Cys).
  Nat Struct Mol Biol, 15, 507-514.  
18222996 C.Slavov, M.Ballottari, T.Morosinotto, R.Bassi, and A.R.Holzwarth (2008).
Trap-limited charge separation kinetics in higher plant photosystem I complexes.
  Biophys J, 94, 3601-3612.  
18632664 E.Romanowska, J.Kargul, M.Powikrowska, G.Finazzi, J.Nield, A.Drozak, and B.Pokorska (2008).
Structural organization of photosynthetic apparatus in agranal chloroplasts of maize.
  J Biol Chem, 283, 26037-26046.  
18433418 E.Ströher, and K.J.Dietz (2008).
The dynamic thiol-disulphide redox proteome of the Arabidopsis thaliana chloroplast as revealed by differential electrophoretic mobility.
  Physiol Plant, 133, 566-583.  
18175204 G.Gulis, K.V.Narasimhulu, L.N.Fox, and K.E.Redding (2008).
Purification of His6-tagged Photosystem I from Chlamydomonas reinhardtii.
  Photosynth Res, 96, 51-60.  
18208520 H.U.Kim, C.van Oostende, G.J.Basset, and J.Browse (2008).
The AAE14 gene encodes the Arabidopsis o-succinylbenzoyl-CoA ligase that is essential for phylloquinone synthesis and photosystem-I function.
  Plant J, 54, 272-283.  
18318833 J.Kargul, and J.Barber (2008).
Photosynthetic acclimation: structural reorganisation of light harvesting antenna--role of redox-dependent phosphorylation of major and minor chlorophyll a/b binding proteins.
  FEBS J, 275, 1056-1068.  
17924203 M.Brecht, J.B.Nieder, H.Studier, E.Schlodder, and R.Bittl (2008).
Red antenna states of photosystem I from Synechococcus sp. PCC 7002.
  Photosynth Res, 95, 155-162.  
18766462 M.Chen, and Y.Zhang (2008).
Tracking the molecular evolution of photosynthesis through characterization of atomic contents of the photosynthetic units.
  Photosynth Res, 97, 255-261.  
18618287 P.Mulo, S.Sirpiö, M.Suorsa, and E.M.Aro (2008).
Auxiliary proteins involved in the assembly and sustenance of photosystem II.
  Photosynth Res, 98, 489-501.  
18458090 T.Tomo, Y.Kato, T.Suzuki, S.Akimoto, T.Okubo, T.Noguchi, K.Hasegawa, T.Tsuchiya, K.Tanaka, M.Fukuya, N.Dohmae, T.Watanabe, and M.Mimuro (2008).
Characterization of highly purified photosystem I complexes from the chlorophyll d-dominated cyanobacterium Acaryochloris marina MBIC 11017.
  J Biol Chem, 283, 18198-18209.  
17955341 T.Wydrzynski, W.Hillier, and B.Conlan (2007).
Engineering model proteins for Photosystem II function.
  Photosynth Res, 94, 225-233.  
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.