2WSC

Improved Model of Plant Photosystem I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.363 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure Determination and Improved Model of Plant Photosystem I.

Amunts, A.Toporik, H.Borovikova, A.Nelson, N.

(2010) J.Biol.Chem. 285: 3478

  • DOI: 10.1074/jbc.M109.072645
  • Primary Citation of Related Structures:  2WSE, 2WSF, 3LW5

  • PubMed Abstract: 
  • Photosystem I functions as a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae, and higher plants. Functionally, Photosystem I captures sunlight and transfers the excitation ener ...

    Photosystem I functions as a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae, and higher plants. Functionally, Photosystem I captures sunlight and transfers the excitation energy through an intricate and precisely organized antenna system, consisting of a pigment network, to the center of the molecule, where it is used in the transmembrane electron transfer reaction. Our current understanding of the sophisticated mechanisms underlying these processes has profited greatly from elucidation of the crystal structures of the Photosystem I complex. In this report, we describe the developments that ultimately led to enhanced structural information of plant Photosystem I. In addition, we report an improved crystallographic model at 3.3-A resolution, which allows analysis of the structure in more detail. An improved electron density map yielded identification and tracing of subunit PsaK. The location of an additional ten beta-carotenes as well as five chlorophylls and several loop regions, which were previously uninterpretable, are now modeled. This represents the most complete plant Photosystem I structure obtained thus far, revealing the locations of and interactions among 17 protein subunits and 193 non-covalently bound photochemical cofactors. Using the new crystal structure, we examine the network of contacts among the protein subunits from the structural perspective, which provide the basis for elucidating the functional organization of the complex.


    Organizational Affiliation

    Biochemistry Department, 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
AT3G54890
1
241Arabidopsis thalianaGene Names: LHCA1 (CAB6)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q01667 (Arabidopsis thaliana)
Go to UniProtKB:  Q01667
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM I
2
269Pisum sativumGene Names: lhaB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q41038 (Pisum sativum)
Go to UniProtKB:  Q41038
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LHCA3
3
276Glycine maxN/A
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for C6TEX2 (Glycine max)
Go to UniProtKB:  C6TEX2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTIC
4
251Pisum sativumGene Names: lhcA-P4
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q9SQL2 (Pisum sativum)
Go to UniProtKB:  Q9SQL2
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
A
758Pisum sativumGene Names: psaA (psaA1)
EC: 1.97.1.12
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P05310 (Pisum sativum)
Go to UniProtKB:  P05310
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
B
734Pisum sativumGene Names: psaB (psaA2)
EC: 1.97.1.12
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P05311 (Pisum sativum)
Go to UniProtKB:  P05311
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I IRON-SULFUR CENTER
C
81Pisum sativumGene Names: psaC (frxA)
EC: 1.97.1.12
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P10793 (Pisum sativum)
Go to UniProtKB:  P10793
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I REACTION CENTER SUBUNIT II, CHLOROPLASTIC
D
212Spinacia oleraceaGene Names: psaD
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P12353 (Spinacia oleracea)
Go to UniProtKB:  P12353
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I REACTION CENTER SUBUNIT IV A, CHLOROPLASTIC
E
143Arabidopsis thalianaGene Names: PSAE1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q9S831 (Arabidopsis thaliana)
Go to UniProtKB:  Q9S831
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTIC
F
231Spinacia oleraceaGene Names: PSAF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P12355 (Spinacia oleracea)
Go to UniProtKB:  P12355
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTIC
G
167Spinacia oleraceaGene Names: PSAG
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P12357 (Spinacia oleracea)
Go to UniProtKB:  P12357
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I REACTION CENTER SUBUNIT VI, CHLOROPLASTIC
H
144Spinacia oleraceaGene Names: PSAH
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P22179 (Spinacia oleracea)
Go to UniProtKB:  P22179
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I REACTION CENTER SUBUNIT VIII
I
40Pisum sativumGene Names: psaI
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P17227 (Pisum sativum)
Go to UniProtKB:  P17227
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I REACTION CENTER SUBUNIT IX
J
44Spinacia oleraceaGene Names: psaJ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P17230 (Spinacia oleracea)
Go to UniProtKB:  P17230
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I REACTION CENTER SUBUNIT PSAK, CHLOROPLASTIC
K
131Hordeum vulgareGene Names: PSAK
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P36886 (Hordeum vulgare)
Go to UniProtKB:  P36886
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I REACTION CENTER SUBUNIT XI, CHLOROPLASTIC
L
216Spinacia oleraceaGene Names: PSAL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q41385 (Spinacia oleracea)
Go to UniProtKB:  Q41385
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I-N SUBUNIT
N
170Phaseolus vulgarisGene Names: PSI-N
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q84U30 (Phaseolus vulgaris)
Go to UniProtKB:  Q84U30
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM I-N SUBUNIT
R
53N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
2, 3, B, H
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
SF4
Query on SF4

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

Download SDF File 
Download CCD File 
A, B
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 
1, 2, 3, 4, A, B, F, G, H, I, J, K, L, R
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
LMG
Query on LMG

Download SDF File 
Download CCD File 
B
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCR
Query on BCR

Download SDF File 
Download CCD File 
3, A, B, I, L
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMU
Query on LMU

Download SDF File 
Download CCD File 
1, 2, 3, 4, A, B, K, L, R
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
R
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.363 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 120.655α = 90.00
b = 189.086β = 91.24
c = 129.388γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2012-08-08
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance