4KT0

Crystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC 6803


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803.

Mazor, Y.Nataf, D.Toporik, H.Nelson, N.

(2014) Elife 3: e01496-e01496

  • DOI: 10.7554/eLife.01496
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Oxygenic photosynthesis supports virtually all life forms on earth. Light energy is converted by two photosystems-photosystem I (PSI) and photosystem II (PSII). Globally, nearly 50% of photosynthesis takes place in the Ocean, where single cell cyanob ...

    Oxygenic photosynthesis supports virtually all life forms on earth. Light energy is converted by two photosystems-photosystem I (PSI) and photosystem II (PSII). Globally, nearly 50% of photosynthesis takes place in the Ocean, where single cell cyanobacteria and algae reside together with their viruses. An operon encoding PSI was identified in cyanobacterial marine viruses. We generated a PSI that mimics the salient features of the viral complex, named PSI(PsaJF). PSI(PsaJF) is promiscuous for its electron donors and can accept electrons from respiratory cytochromes. We solved the structure of PSI(PsaJF) and a monomeric PSI, with subunit composition similar to the viral PSI, providing for the first time a detailed description of the reaction center and antenna system from mesophilic cyanobacteria, including red chlorophylls and cofactors of the electron transport chain. Our finding extends the understanding of PSI structure, function and evolution and suggests a unique function for the viral PSI. DOI: http://dx.doi.org/10.7554/eLife.01496.001.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A1
A
751Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaA
EC: 1.97.1.12
Find proteins for P29254 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P29254
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A2
B
731Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaB
EC: 1.97.1.12
Find proteins for P29255 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P29255
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem I iron-sulfur center
C
81Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaC
EC: 1.97.1.12
Find proteins for P32422 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P32422
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem I subunit II
D
141Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaD
Find proteins for P19569 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P19569
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IV
E
74Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaE
Find proteins for P12975 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P12975
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Photosystem I subunit III
F
165Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaF
Find proteins for P29256 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P29256
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IX
J
40Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaJ
Find proteins for Q55329 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  Q55329
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit PsaK
K
128Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaK2
Find proteins for P74564 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P74564
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit XII
M
31Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaM
Find proteins for P72986 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P72986
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PQN
Query on PQN

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Download CCD File 
A, B
PHYLLOQUINONE
VITAMIN K1; 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
CLA
Query on CLA

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Download CCD File 
A, B, F, J, K
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
CL0
Query on CL0

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Download CCD File 
A
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
LMG
Query on LMG

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Download CCD File 
B
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCR
Query on BCR

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A, B, F, J
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LHG
Query on LHG

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Download CCD File 
A, B
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
LMU
Query on LMU

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Download CCD File 
B, J
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 120.179α = 90.00
b = 173.308β = 90.00
c = 179.136γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
XDSdata scaling
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references