1QZV

Crystal structure of plant photosystem I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.44 Å
  • R-Value Free: 0.420 
  • R-Value Work: 0.410 
  • R-Value Observed: 0.410 

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This is version 2.0 of the entry. See complete history


Literature

Crystal structure of plant photosystem I.

Ben-Shem, A.Frolow, F.Nelson, N.

(2003) Nature 426: 630-635

  • DOI: https://doi.org/10.1038/nature02200
  • Primary Citation of Related Structures:  
    1QZV

  • PubMed Abstract: 

    Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4 A resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.


  • Organizational Affiliation

    Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAAA,
Q [auth P]
726Pisum sativumMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSABB,
R [auth Q]
732Pisum sativumMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSACC,
S [auth R]
80Pisum sativumMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSADD,
T [auth S]
154Pisum sativumMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAEE,
U [auth T]
64Pisum sativumMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAFF,
V [auth U]
154Pisum sativumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAGG,
W [auth V]
74Pisum sativumMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAHH,
X [auth W]
52Pisum sativumMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAI
I, Y
30Pisum sativumMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAJ
J, Z
41Pisum sativumMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAKAA [auth 5],
K
42Pisum sativumMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSALBA [auth 6],
L
135Pisum sativumMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA1CA [auth 7],
M [auth 1]
109Pisum sativumMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA2DA [auth 8],
N [auth 2]
115Pisum sativumMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA3EA [auth 9],
O [auth 3]
117Pisum sativumMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA4FA [auth 0],
P [auth 4]
119Pisum sativumMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
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AB [auth A]
AC [auth A]
AD [auth B]
AE [auth F]
AF [auth 1]
AB [auth A],
AC [auth A],
AD [auth B],
AE [auth F],
AF [auth 1],
AG [auth 3],
AH [auth P],
AI [auth P],
AJ [auth Q],
AK [auth Q],
AL [auth 5],
AM [auth 8],
AN [auth 0],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth F],
BF [auth 1],
BG [auth 3],
BH [auth P],
BI [auth P],
BJ [auth Q],
BK [auth Q],
BL [auth 5],
BM [auth 8],
BN [auth 0],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth F],
CF [auth 1],
CG [auth 3],
CH [auth P],
CI [auth P],
CJ [auth Q],
CK [auth Q],
CL [auth 6],
CM [auth 8],
CN [auth 0],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth G],
DF [auth 2],
DG [auth 3],
DH [auth P],
DI [auth P],
DJ [auth Q],
DK [auth Q],
DL [auth 6],
DM [auth 8],
DN [auth 0],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth G],
EF [auth 2],
EG [auth 3],
EH [auth P],
EI [auth P],
EJ [auth Q],
EK [auth Q],
EL [auth 6],
EM [auth 8],
EN [auth 0],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth H],
FF [auth 2],
FG [auth 3],
FH [auth P],
FI [auth P],
FJ [auth Q],
FK [auth Q],
FL [auth 6],
FM [auth 8],
FN [auth 0],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GE [auth J],
GF [auth 2],
GG [auth 4],
GH [auth P],
GI [auth P],
GJ [auth Q],
GK [auth Q],
GL [auth 7],
GM [auth 8],
GN [auth 0],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth J],
HF [auth 2],
HG [auth 4],
HH [auth P],
HI [auth P],
HJ [auth Q],
HK [auth Q],
HL [auth 7],
HM [auth 8],
HN [auth 0],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth J],
IF [auth 2],
IG [auth 4],
IH [auth P],
II [auth P],
IJ [auth Q],
IK [auth Q],
IL [auth 7],
IM [auth 9],
IN [auth 0],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JE [auth K],
JF [auth 2],
JG [auth 4],
JH [auth P],
JI [auth P],
JJ [auth Q],
JL [auth 7],
JM [auth 9],
JN [auth 0],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth K],
KF [auth 2],
KG [auth 4],
KH [auth P],
KI [auth P],
KJ [auth Q],
KK [auth Q],
KL [auth 7],
KM [auth 9],
KN [auth 0],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LE [auth K],
LF [auth 2],
LG [auth 4],
LH [auth P],
LI [auth P],
LJ [auth Q],
LL [auth 7],
LM [auth 9],
LN [auth 0],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth L],
MF [auth 2],
MG [auth 4],
MH [auth P],
MI [auth P],
MJ [auth Q],
ML [auth 7],
MM [auth 9],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth L],
NF [auth 2],
NG [auth 4],
NH [auth P],
NJ [auth Q],
NK [auth U],
NL [auth 7],
NM [auth 9],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OE [auth L],
OF [auth 2],
OG [auth 4],
OH [auth P],
OJ [auth Q],
OK [auth U],
OL [auth 7],
OM [auth 9],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth L],
PF [auth 2],
PG [auth 4],
PH [auth P],
PI [auth P],
PJ [auth Q],
PK [auth U],
PL [auth 7],
PM [auth 9],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth 1],
QF [auth 2],
QG [auth 4],
QH [auth P],
QI [auth P],
QJ [auth Q],
QK [auth U],
QL [auth 7],
QM [auth 9],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RE [auth 1],
RF [auth 2],
RG [auth 4],
RH [auth P],
RI [auth Q],
RJ [auth Q],
RK [auth U],
RL [auth 7],
RM [auth 9],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SE [auth 1],
SF [auth 3],
SG [auth 4],
SH [auth P],
SI [auth Q],
SJ [auth Q],
SK [auth U],
SL [auth 7],
SM [auth 9],
TA [auth A],
TB [auth A],
TC [auth B],
TE [auth 1],
TF [auth 3],
TG [auth 4],
TH [auth P],
TI [auth Q],
TJ [auth Q],
TK [auth V],
TL [auth 8],
TM [auth 9],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UE [auth 1],
UF [auth 3],
UG [auth 4],
UH [auth P],
UI [auth Q],
UJ [auth Q],
UK [auth V],
UL [auth 8],
UM [auth 9],
VA [auth A],
VB [auth A],
VC [auth B],
VE [auth 1],
VF [auth 3],
VG [auth 4],
VH [auth P],
VI [auth Q],
VJ [auth Q],
VK [auth W],
VL [auth 8],
VM [auth 9],
WA [auth A],
WB [auth A],
WC [auth B],
WE [auth 1],
WF [auth 3],
WG [auth P],
WH [auth P],
WI [auth Q],
WJ [auth Q],
WK [auth Z],
WL [auth 8],
WM [auth 0],
XA [auth A],
XC [auth B],
XD [auth F],
XE [auth 1],
XF [auth 3],
XG [auth P],
XH [auth P],
XI [auth Q],
XJ [auth Q],
XK [auth Z],
XL [auth 8],
XM [auth 0],
YA [auth A],
YC [auth B],
YD [auth F],
YE [auth 1],
YF [auth 3],
YG [auth P],
YH [auth P],
YI [auth Q],
YJ [auth Q],
YK [auth Z],
YL [auth 8],
YM [auth 0],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth F],
ZE [auth 1],
ZF [auth 3],
ZG [auth P],
ZH [auth P],
ZI [auth Q],
ZJ [auth Q],
ZK [auth 5],
ZL [auth 8],
ZM [auth 0]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PQN
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JK [auth Q],
NI [auth P],
TD [auth B],
XB [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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LK [auth R]
MK [auth R]
OI [auth P]
VD [auth C]
WD [auth C]
LK [auth R],
MK [auth R],
OI [auth P],
VD [auth C],
WD [auth C],
YB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.44 Å
  • R-Value Free: 0.420 
  • R-Value Work: 0.410 
  • R-Value Observed: 0.410 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.283α = 90
b = 190.376β = 90.48
c = 220.253γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-07-25
    Changes: Non-polymer description
  • Version 2.0: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Non-polymer description