2O01

The Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.409 
  • R-Value Work: 0.348 
  • R-Value Observed: 0.351 

Starting Model: experimental
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Literature

The structure of a plant photosystem I supercomplex at 3.4 A resolution.

Amunts, A.Drory, O.Nelson, N.

(2007) Nature 447: 58-63

  • DOI: https://doi.org/10.1038/nature05687
  • Primary Citation of Related Structures:  
    2O01

  • PubMed Abstract: 

    All higher organisms on Earth receive energy directly or indirectly from oxygenic photosynthesis performed by plants, green algae and cyanobacteria. Photosystem I (PSI) is a supercomplex of a reaction centre and light-harvesting complexes. It generates the most negative redox potential in nature, and thus largely determines the global amount of enthalpy in living systems. We report the structure of plant PSI at 3.4 A resolution, revealing 17 protein subunits. PsaN was identified in the luminal side of the supercomplex, and most of the amino acids in the reaction centre were traced. The crystal structure of PSI provides a picture at near atomic detail of 11 out of 12 protein subunits of the reaction centre. At this level, 168 chlorophylls (65 assigned with orientations for Q(x) and Q(y) transition dipole moments), 2 phylloquinones, 3 Fe(4)S(4) clusters and 5 carotenoids are described. This structural information extends the understanding of the most efficient nano-photochemical machine in nature.


  • Organizational Affiliation

    Department of Biochemistry, The George S. Wise Faculty of Life Sciences, The Daniella Rich Institute for Structural Biology, Tel Aviv University, Tel Aviv, 69978, Israel.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1754Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05310 (Pisum sativum)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2732Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05311 (Pisum sativum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P10793 (Pisum sativum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplast138Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV A, chloroplast62Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplast154Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplast95Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplast75Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII30Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX42Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplast38Arabidopsis thalianaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplast164Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I-N subunitM [auth N]85Phaseolus vulgarisMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
AT3g54890N [auth 1]187Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Type II chlorophyll a/b binding protein from photosystem IO [auth 2]186Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PSI type III chlorophyll a/b-binding proteinP [auth 3]165Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PSI light-harvesting antenna chlorophyll a/b-binding proteinQ [auth 4]165Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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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],
AF [auth 2],
AG [auth 4],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth K],
BF [auth 2],
BG [auth 4],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth K],
CF [auth 2],
CG [auth 4],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth L],
DF [auth 2],
DG [auth 4],
EA [auth A],
EB [auth A],
EC [auth B],
EE [auth L],
EF [auth 2],
EG [auth 4],
FA [auth A],
FB [auth A],
FC [auth B],
FE [auth L],
FF [auth 2],
FG [auth 4],
GA [auth A],
GB [auth A],
GC [auth B],
GE [auth L],
GF [auth 2],
GG [auth 4],
HA [auth A],
HB [auth A],
HC [auth B],
HE [auth L],
HF [auth 2],
HG [auth 4],
IA [auth A],
IB [auth A],
IC [auth B],
IF [auth 2],
IG [auth 4],
JA [auth A],
JC [auth B],
JD [auth F],
JE [auth 1],
JF [auth 3],
JG [auth 4],
KA [auth A],
KC [auth B],
KD [auth F],
KE [auth 1],
KF [auth 3],
KG [auth 4],
LA [auth A],
LB [auth B],
LC [auth B],
LD [auth F],
LE [auth 1],
LF [auth 3],
LG [auth 4],
MA [auth A],
MB [auth B],
MC [auth B],
MD [auth F],
ME [auth 1],
MF [auth 3],
MG [auth 4],
NA [auth A],
NB [auth B],
NC [auth B],
ND [auth F],
NE [auth 1],
NF [auth 3],
OA [auth A],
OB [auth B],
OC [auth B],
OD [auth F],
OE [auth 1],
OF [auth 3],
PA [auth A],
PB [auth B],
PC [auth B],
PD [auth F],
PE [auth 1],
PF [auth 3],
QA [auth A],
QB [auth B],
QC [auth B],
QE [auth 1],
QF [auth 3],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
RD [auth G],
RE [auth 1],
RF [auth 3],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
SD [auth G],
SE [auth 1],
SF [auth 3],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
TD [auth H],
TE [auth 1],
TF [auth 3],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
UD [auth H],
UE [auth 1],
UF [auth 3],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VD [auth I],
VE [auth 1],
VF [auth 3],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WE [auth 2],
WF [auth 3],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XD [auth J],
XE [auth 2],
XF [auth 3],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YD [auth J],
YE [auth 2],
YF [auth 4],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth J],
ZE [auth 2],
ZF [auth 4]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
BCR
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GD [auth B],
IE [auth L],
KB [auth A],
QD [auth F],
WD [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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FD [auth B],
JB [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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ED [auth B],
HD [auth C],
ID [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.409 
  • R-Value Work: 0.348 
  • R-Value Observed: 0.351 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.054α = 90
b = 188.784β = 95.19
c = 127.518γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2007-11-14
    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: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description