1QZV | pdb_00001qzv

Crystal structure of plant photosystem I

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 771.33 kDa 
  • Atom Count: 13,938 
  • Modeled Residue Count: 5,488 
  • Deposited Residue Count: 5,488 
  • Unique protein chains: 16

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAAA,
Q [auth P]		726Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSABB,
R [auth Q]		732Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSACC,
S [auth R]		80Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSADD,
T [auth S]		154Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAEE,
U [auth T]		64Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAFF,
V [auth U]		154Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAGG,
W [auth V]		74Lathyrus oleraceusMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAHH,
X [auth W]		52Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAI
I, Y
30Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAJ
J, Z
41Lathyrus oleraceusMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSAKAA [auth 5],
K		42Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT PHOTOSYSTEM I: SUBUNIT PSALBA [auth 6],
L		135Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA1CA [auth 7],
M [auth 1]		109Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA2DA [auth 8],
N [auth 2]		115Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA3EA [auth 9],
O [auth 3]		117Lathyrus oleraceusMutation(s): 0 
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|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA4FA [auth 0],
P [auth 4]		119Lathyrus oleraceusMutation(s): 0 

Small Molecules

Ligands 3 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 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

Query on PQN


Download:Ideal Coordinates CCD File
JK [auth Q],
NI [auth P],
TD [auth B],
XB [auth A]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
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 (Depositor) 
  • R-Value Work:  0.410 (Depositor) 
  • R-Value Observed: 0.410 (Depositor) 
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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View more in-depth experimental data

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