4L6V | pdb_00004l6v

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 (Depositor), 0.303 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.7554/eLife.01496
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 1,036.49 kDa 
  • Atom Count: 68,370 
  • Modeled Residue Count: 6,534 
  • Deposited Residue Count: 6,777 
  • Unique protein chains: 10

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
I [auth a],
R [auth 1]		751Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaA, BEST7613_2234, MYO_18690
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
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UniProt GroupP29254
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
J [auth b],
S [auth 2]		731Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaB, BEST7613_2235, MYO_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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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC,
K [auth c],
T [auth 3]		81Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaC, BEST7613_5694, MYO_120930
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P32422 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I subunit IID,
L [auth d],
U [auth 4]		141Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaE, BEST7613_5968, MYO_118260
EC: 1.97.1.12
UniProt
Find proteins for P19569 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE,
M [auth e],
V [auth 5]		74Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaF, BEST7613_2928
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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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Fusion protein of Photosystem I subunit III and subunit IXF,
N [auth f],
W [auth 6]		125Synechocystis sp. PCC 6803, Bacillus subtilis BEST7613
This entity is chimeric		Mutation(s): 1 
Gene Names: psaL, BEST7613_4425, MYO_131030, psaF, BEST7613_2928
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29256 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P29256 
Go to UniProtKB:  P29256
Find proteins for Q55329 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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UniProt GroupsP29256Q55329
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIG [auth L],
P [auth l],
Y [auth 8]		157Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psbM, psaM, BEST7613_1787, MYO_14340
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P37277 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIH [auth M],
Q [auth m],
Z [auth 7]		31Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaF, BEST7613_2928
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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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I subunit IIIBA [auth I],
O [auth i],
X [auth 9]		40Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaI, BEST7613_4424, MYO_131040
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q55330 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q55330 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIAA [auth K],
CA [auth k],
DA [auth 0]		128Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaD, BEST7613_1459, MYO_11100
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P74564 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P74564 
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AB [auth A]
AC [auth A]
AD [auth B]
AE [auth B]
AG [auth a]
AB [auth A],
AC [auth A],
AD [auth B],
AE [auth B],
AG [auth a],
AI [auth b],
AJ [auth l],
AK [auth 1],
AL [auth 1],
AM [auth 2],
AN [auth 2],
BB [auth A],
BC [auth A],
BD [auth B],
BE [auth B],
BF [auth a],
BG [auth a],
BI [auth b],
BK [auth 1],
BL [auth 1],
BM [auth 2],
BN [auth 2],
CB [auth A],
CC [auth A],
CD [auth B],
CE [auth B],
CF [auth a],
CG [auth a],
CI [auth b],
CK [auth 1],
CL [auth 1],
CM [auth 2],
CN [auth 2],
DB [auth A],
DC [auth A],
DD [auth B],
DE [auth B],
DF [auth a],
DG [auth a],
DI [auth b],
DK [auth 1],
DL [auth 1],
DM [auth 2],
DN [auth 2],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth B],
EE [auth B],
EF [auth a],
EG [auth a],
EH [auth b],
EI [auth b],
EJ [auth 1],
EK [auth 1],
EL [auth 1],
EM [auth 2],
EN [auth 2],
FB [auth A],
FC [auth A],
FD [auth B],
FE [auth B],
FF [auth a],
FG [auth a],
FH [auth b],
FI [auth b],
FK [auth 1],
FL [auth 1],
FM [auth 2],
FN [auth 2],
GB [auth A],
GD [auth B],
GF [auth a],
GG [auth a],
GH [auth b],
GI [auth b],
GK [auth 1],
GM [auth 2],
HB [auth A],
HD [auth B],
HF [auth a],
HG [auth a],
HH [auth b],
HI [auth b],
HK [auth 1],
HM [auth 2],
IB [auth A],
ID [auth B],
IF [auth a],
IG [auth a],
IH [auth b],
II [auth b],
IK [auth 1],
IM [auth 2],
JB [auth A],
JD [auth B],
JF [auth a],
JG [auth a],
JH [auth b],
JI [auth b],
JK [auth 1],
JM [auth 2],
KB [auth A],
KD [auth B],
KF [auth a],
KG [auth a],
KH [auth b],
KI [auth b],
KK [auth 1],
KM [auth 2],
LB [auth A],
LD [auth B],
LE [auth L],
LF [auth a],
LG [auth a],
LH [auth b],
LI [auth b],
LK [auth 1],
LM [auth 2],
LN [auth 8],
MB [auth A],
MD [auth B],
ME [auth L],
MF [auth a],
MG [auth a],
MH [auth b],
MI [auth b],
MK [auth 1],
MM [auth 2],
MN [auth 8],
NB [auth A],
ND [auth B],
NE [auth L],
NF [auth a],
NG [auth a],
NH [auth b],
NI [auth b],
NK [auth 1],
NM [auth 2],
NN [auth 8],
OA [auth A],
OB [auth A],
OD [auth B],
OF [auth a],
OG [auth a],
OH [auth b],
OI [auth b],
OJ [auth 1],
OK [auth 1],
OM [auth 2],
PA [auth A],
PB [auth A],
PD [auth B],
PF [auth a],
PG [auth a],
PH [auth b],
PI [auth b],
PJ [auth 1],
PK [auth 1],
PM [auth 2],
QA [auth A],
QB [auth A],
QD [auth B],
QF [auth a],
QG [auth a],
QH [auth b],
QI [auth b],
QJ [auth 1],
QK [auth 1],
QM [auth 2],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RE [auth a],
RF [auth a],
RG [auth a],
RH [auth b],
RI [auth b],
RJ [auth 1],
RK [auth 1],
RL [auth 2],
RM [auth 2],
RN [auth K],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SF [auth a],
SG [auth a],
SH [auth b],
SI [auth b],
SJ [auth 1],
SK [auth 1],
SL [auth 2],
SM [auth 2],
SN [auth K],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TF [auth a],
TH [auth b],
TJ [auth 1],
TK [auth 1],
TL [auth 2],
TM [auth 2],
TN [auth k],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth a],
UH [auth b],
UJ [auth 1],
UK [auth 1],
UL [auth 2],
UM [auth 2],
UN [auth k],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VF [auth a],
VH [auth b],
VJ [auth 1],
VK [auth 1],
VL [auth 2],
VM [auth 2],
VN [auth 0],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WF [auth a],
WH [auth b],
WJ [auth 1],
WK [auth 1],
WL [auth 2],
WM [auth 2],
WN [auth 0],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XF [auth a],
XH [auth b],
XJ [auth 1],
XK [auth 1],
XL [auth 2],
XM [auth 2],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YF [auth a],
YH [auth b],
YI [auth l],
YJ [auth 1],
YK [auth 1],
YL [auth 2],
YM [auth 2],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZF [auth a],
ZH [auth b],
ZI [auth l],
ZJ [auth 1],
ZK [auth 1],
ZL [auth 2],
ZM [auth 2]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG


Download:Ideal Coordinates CCD File
CH [auth b],
PC [auth B],
PL [auth 2]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG


Download:Ideal Coordinates CCD File
AF [auth a]
DH [auth b]
MA [auth A]
MJ [auth 1]
NA [auth A]
AF [auth a],
DH [auth b],
MA [auth A],
MJ [auth 1],
NA [auth A],
NJ [auth 1],
QC [auth B],
QL [auth 2],
ZE [auth a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR

Query on BCR


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AH [auth b]
BH [auth b]
BJ [auth l]
CJ [auth l]
DJ [auth m]
AH [auth b],
BH [auth b],
BJ [auth l],
CJ [auth l],
DJ [auth m],
HA [auth A],
HC [auth B],
HJ [auth 1],
HL [auth 2],
IA [auth A],
IC [auth B],
IE [auth F],
IJ [auth 1],
IL [auth 2],
IN [auth 6],
JA [auth A],
JC [auth B],
JE [auth F],
JJ [auth 1],
JL [auth 2],
JN [auth 6],
KA [auth A],
KC [auth B],
KE [auth F],
KJ [auth 1],
KL [auth 2],
KN [auth 6],
LA [auth A],
LC [auth B],
LJ [auth 1],
LL [auth 2],
MC [auth B],
ML [auth 2],
NC [auth B],
NL [auth 2],
OC [auth B],
OE [auth L],
OL [auth 2],
ON [auth 8],
PE [auth L],
PN [auth 8],
QE [auth M],
QN [auth 7],
UE [auth a],
UG [auth b],
VE [auth a],
VG [auth b],
VI [auth f],
WE [auth a],
WG [auth b],
WI [auth f],
XE [auth a],
XG [auth b],
XI [auth f],
YE [auth a],
YG [auth b],
ZG [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
FA [auth A]
FJ [auth 1]
GC [auth B]
GL [auth 2]
SE [auth a]
FA [auth A],
FJ [auth 1],
GC [auth B],
GL [auth 2],
SE [auth a],
TG [auth b]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
GA [auth A]
GE [auth C]
GJ [auth 1]
GN [auth 3]
HE [auth C]
GA [auth A],
GE [auth C],
GJ [auth 1],
GN [auth 3],
HE [auth C],
HN [auth 3],
TE [auth a],
TI [auth c],
UI [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.297 (Depositor), 0.303 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
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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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • 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