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
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P05310 
Go to UniProtKB:  P05310
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05310
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P05311 
Go to UniProtKB:  P05311
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05311
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P10793 
Go to UniProtKB:  P10793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10793
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplast138Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12353 (Spinacia oleracea)
Explore P12353 
Go to UniProtKB:  P12353
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12353
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV A, chloroplast62Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9S831 (Arabidopsis thaliana)
Explore Q9S831 
Go to UniProtKB:  Q9S831
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S831
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplast154Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12355 (Spinacia oleracea)
Explore P12355 
Go to UniProtKB:  P12355
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12355
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplast95Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12357 (Spinacia oleracea)
Explore P12357 
Go to UniProtKB:  P12357
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12357
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplast75Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P22179 (Spinacia oleracea)
Explore P22179 
Go to UniProtKB:  P22179
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22179
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P17227 
Go to UniProtKB:  P17227
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17227
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX42Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17230 (Spinacia oleracea)
Explore P17230 
Go to UniProtKB:  P17230
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17230
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplast38Arabidopsis thalianaMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplast164Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q41385 (Spinacia oleracea)
Explore Q41385 
Go to UniProtKB:  Q41385
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41385
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I-N subunitM [auth N]85Phaseolus vulgarisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q84U30 (Phaseolus vulgaris)
Explore Q84U30 
Go to UniProtKB:  Q84U30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84U30
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
AT3g54890N [auth 1]187Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q01667 (Arabidopsis thaliana)
Explore Q01667 
Go to UniProtKB:  Q01667
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01667
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for Q41038 (Pisum sativum)
Explore Q41038 
Go to UniProtKB:  Q41038
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41038
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PSI type III chlorophyll a/b-binding proteinP [auth 3]165Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SY97 (Arabidopsis thaliana)
Explore Q9SY97 
Go to UniProtKB:  Q9SY97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SY97
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore Q9SQL2 
Go to UniProtKB:  Q9SQL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SQL2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 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],
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
Query on BCR

Download Ideal Coordinates CCD File 
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

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

Download Ideal Coordinates CCD File 
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

View Full Validation Report



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
  • Version 3.0: 2024-12-25
    Changes: Advisory, Atomic model, Derived calculations, Structure summary