4L6V

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  
    4KT0, 4L6V

  • 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
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I subunit II4Dd141Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaEBEST7613_5968MYO_118260
EC: 1.97.1.12
Find proteins for P19569 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV5Ee74Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaFBEST7613_2928
EC: 1.97.1.12
Find proteins for P12975 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion protein of Photosystem I subunit III and subunit IX6Ff125Synechocystis sp. PCC 6803Bacillus subtilis BEST7613
This entity is chimeric
Mutation(s): 1 
Gene Names: psaLBEST7613_4425MYO_131030
EC: 1.97.1.12
Find proteins for P29256 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Go to UniProtKB:  P29256
Find proteins for Q55329 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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  • Reference Sequence
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII7Mm31Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaFBEST7613_2928
EC: 1.97.1.12
Find proteins for P72986 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I subunit III9Ii40Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaIBEST7613_4424MYO_131040
EC: 1.97.1.12
Find proteins for Q55330 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII0Kk128Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaDBEST7613_1459MYO_11100
EC: 1.97.1.12
Find proteins for P74564 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A11Aa751Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaABEST7613_2234MYO_18690
EC: 1.97.1.12
Find proteins for P29254 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A22Bb731Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaBBEST7613_2235MYO_18700
EC: 1.97.1.12
Find proteins for P29255 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center3Cc81Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaCBEST7613_5694MYO_120930
EC: 1.97.1.12
Find proteins for P32422 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI8Ll157Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psbMpsaMBEST7613_1787MYO_14340
EC: 1.97.1.12
Find proteins for P37277 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download CCD File 
0, 1, 2, 8, A, B, K, L, a, b, k, l
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
LMG
Query on LMG

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2, B, b
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
LHG
Query on LHG

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

Download CCD File 
1, 2, 6, 7, 8, A, B, F, L, M, a, b, f, l, m
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PQN
Query on PQN

Download CCD File 
1, 2, A, B, a, b
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
1, 3, A, C, a, c
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 214.619α = 90
b = 133.68β = 111.14
c = 219.846γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
REFMACrefinement
XDSdata scaling
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-05-07
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description