4KT0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 ?
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/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 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1751Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: BEST7613_2234MYO_18690psaA
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29254 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P29254 
Go to UniProtKB:  P29254
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29254
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2731Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaBBEST7613_2235MYO_18700
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29255 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Go to UniProtKB:  P29255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29255
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaCBEST7613_5694MYO_120930
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P32422 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P32422 
Go to UniProtKB:  P32422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32422
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I subunit II141Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaDBEST7613_1459MYO_11100
EC: 1.97.1.12
UniProt
Find proteins for P19569 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P19569 
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UniProt GroupP19569
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV74Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaEBEST7613_5968MYO_118260
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P12975 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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UniProt GroupP12975
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I subunit III165Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaFBEST7613_2928
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29256 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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UniProt GroupP29256
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXG [auth J]40Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaJBEST7613_2927MYO_115450
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q55329 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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UniProt GroupQ55329
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKH [auth K]128Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaKBEST7613_4536MYO_129960
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P74564 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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UniProt GroupP74564
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIII [auth M]31Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psbMpsaMBEST7613_1787MYO_14340
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P72986 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P72986 
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Entity Groups  
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UniProt GroupP72986
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth K]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth K],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
DB [auth A],
DC [auth B],
DD [auth B],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
KA [auth A],
KC [auth B],
KD [auth B],
LA [auth A],
LB [auth B],
LC [auth B],
LD [auth B],
MA [auth A],
MC [auth B],
MD [auth B],
NA [auth A],
NC [auth B],
OA [auth A],
OC [auth B],
PA [auth A],
PC [auth B],
QA [auth A],
QC [auth B],
QD [auth F],
RA [auth A],
RC [auth B],
SA [auth A],
SC [auth B],
TA [auth A],
TC [auth B],
TD [auth F],
U [auth A],
UA [auth A],
UC [auth B],
UD [auth F],
V [auth A],
VA [auth A],
VC [auth B],
VD [auth J],
W [auth A],
WA [auth A],
WC [auth B],
X [auth A],
XA [auth A],
XC [auth B],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YD [auth J],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth K]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

Download Ideal Coordinates CCD File 
DA [auth A],
M [auth A]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

Download Ideal Coordinates CCD File 
OB [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
KB [auth A],
L [auth A],
N [auth A],
PB [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
O [auth A]
P [auth A]
Q [auth A]
QB [auth B]
R [auth A]
O [auth A],
P [auth A],
Q [auth A],
QB [auth B],
R [auth A],
RB [auth B],
RD [auth F],
S [auth A],
SB [auth B],
SD [auth F],
T [auth A],
TB [auth B],
UB [auth B],
VB [auth B],
WB [auth B],
XB [auth B],
XD [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

Download Ideal Coordinates CCD File 
MB [auth B],
WD [auth J]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
Query on PQN

Download Ideal Coordinates CCD File 
J [auth A],
NB [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
K [auth A],
OD [auth C],
PD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
ND [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 ?
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( ? )Angle ( ? )
a = 120.179¦Á = 90
b = 173.308¦Â = 90
c = 179.136¦Ã = 90
Software Package:
Software NamePurpose
XDSdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 2.0: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
  • Version 2.1: 2024-03-13
    Changes: Source and taxonomy
  • Version 2.2: 2024-11-06
    Changes: Structure summary
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