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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/nature02200

  • 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 cryst ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAA
A, P
726N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAB
B, Q
732N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAC
C, R
80N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAD
D, S
154N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAE
E, T
64N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAF
F, U
154N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAG
G, V
74N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAH
H, W
52N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAI
I, Y
30N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAJ
J, Z
41N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAK
K, 5
42N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PLANT PHOTOSYSTEM I: SUBUNIT PSAL
L, 6
135N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA1
1, 7
109N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA2
2, 8
115N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA3
3, 9
117N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
PLANT LIGHT HARVESTING COMPLEX I(LHCI): SUBUNIT LHCA4
4, 0
119N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, C, P, R
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PQN
Query on PQN

Download SDF File 
Download CCD File 
A, B, P, Q
PHYLLOQUINONE
VITAMIN K1; 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
CLA
Query on CLA

Download SDF File 
Download CCD File 
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, F, G, H, J, K, L, P, Q, U, V, W, Z
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, P, Q, R, S, T, U, V, W, Y, Z
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.44 Å
  • R-Value Free: 0.420 
  • R-Value Work: 0.410 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 182.283α = 90.00
b = 190.376β = 90.48
c = 220.253γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-07-25
    Type: Non-polymer description