All structure family : Photosystem I PsaD, reaction center subunit II
 
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Entry Information
Entry status  (1)
REL
(13)
 
Experimental methods  (1)
X-ray diffraction
(13)
 
Authors  (24)
Nelson N
(11)
Borovikova A
(7)
Toporik H
(6)
Amunts A
(5)
Mazor Y
(5)
Borovikov A
(3)
Caspy I
(2)
Nataf D
(2)
Brovikov A
(1)
Drory O
(1)
Fromme P
(1)
Greenberg I
(1)
Jordan P
(1)
Klaiman D
(1)
Klukas O
(1)
Krauss N
(1)
Kuang T
(1)
Malavath T
(1)
Netzer-El SY
(1)
Qin X
(1)
Saenger W
(1)
Shen JR
(1)
Suga M
(1)
Witt HT
(1)
 
Homo / hetero assembly  (1)
hetero
(13)
 
Assembly composition  (1)
protein/protein complex
(13)
 
Assembly polymer count  (7)
octadecamer
(4)
hexadecamer
(3)
heptadecamer
(2)
33-mer
(1)
36-mer
(1)
decamer
(1)
nonamer
(1)
 
Resolution distribution
2.0 - 2.5
(1)
2.5 - 3
(6)
3.0 - 3.5
(5)
3.5 - 4
(1)
 
Release year distribution
2000 - 2005
(1)
2005 - 2010
(5)
2010 - 2015
(6)
2015 - 2020
(5)
 
Journal  (7)
J Biol Chem
(4)
Elife
(3)
Nature
(2)
Biochim Biophys Acta Bioenerg
(1)
Nat Plants
(1)
Science
(1)
To be published
(1)
 
Macromolecules
Organism superkingdom  (2)
Eukaryota
(9)
Bacteria
(4)
 
Organism name  (4)
Pisum sativum
(5)
Spinacia oleracea
(4)
Synechocystis sp. PCC 6803
(3)
Synechococcus elongatus
(1)
 
Molecule name  (7)
Photosystem I reaction center subunit II, chloroplastic
(9)
PSI-D
(8)
Photosystem I 16 kDa polypeptide
(4)
Photosystem I 20 kDa subunit
(4)
Photosystem I reaction center subunit II
(4)
Uncharacterized protein
(4)
Photosystem I subunit PsaD
(1)
 
Molecule type  (1)
Protein
(13)
 
Gene names  (4)
psaD
(9)
slr0737
(3)
GLYMA_10G249000
(1)
tll1724
(1)
 
Interacting Molecules  (32)
Photosystem I P700 chlorophyll a apoprotein A1
(13)
Photosystem I P700 chlorophyll a apoprotein A2
(13)
Photosystem I iron-sulfur center
(13)
Photosystem I reaction center subunit IX
(13)
Photosystem I reaction center subunit VIII
(12)
Chlorophyll a-b binding protein P4, chloroplastic
(9)
Chlorophyll a-b binding protein, chloroplastic
(9)
Photosystem I reaction center subunit IV
(9)
Photosystem I reaction center subunit III
(7)
Photosystem I reaction center subunit V, chloroplastic
(7)
Photosystem I reaction center subunit III, chloroplastic
(6)
Photosystem I-N subunit
(6)
Chlorophyll a-b binding protein 3, chloroplastic
(5)
Chlorophyll a-b binding protein 6, chloroplastic
(5)
PSI subunit V
(5)
PSI-K
(5)
Photosystem I reaction center subunit VI
(5)
Photosystem I reaction center subunit IV A, chloroplastic
(4)
Photosystem I reaction center subunit VI, chloroplastic
(4)
Photosystem I reaction center subunit XI, chloroplastic
(4)
Photosystem I reaction center subunit XII
(4)
PHOTOSYSTEM I-N SUBUNIT
(3)
Photosystem I reaction center subunit PsaK 2
(3)
Photosystem I reaction center subunit XI
(3)
Photosystem I reaction center subunit psaK, chloroplastic
(3)
Photosystem I reaction center subunit V
(2)
CHAIN R
(1)
Photosystem I 4.8K protein
(1)
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
(1)
Photosystem I reaction center subunit II
(1)
Photosystem I reaction center subunit PsaK
(1)
Photosystem I reaction center subunit psaK, chloroplast
(1)
 
Interacting ligands  (1)
ACT : ACETATE ION
(1)
 
Function and Biology
EC number / name  (1)
1.97.1.12 : Photosystem I
(2)
 
Biological function  (1)
protein binding
(6)
 
Biological process  (1)
photosynthesis
(13)
 
Biological cell component  (7)
photosystem I
(13)
photosystem I reaction center
(13)
chloroplast thylakoid membrane
(7)
thylakoid
(7)
chloroplast
(3)
membrane
(3)
plasma membrane
(3)
 
Sequence and Structure classification
SCOP fold  (1)
Photosystem I subunit PsaD
(1)
 
SCOP family  (1)
Photosystem I subunit PsaD
(1)
 
CATH class  (1)
Alpha Beta
(13)
 
CATH topology  (1)
Photosystem 1 Reaction Centre Subunit Ii; Chain: D;
(13)
 
Pfam accession / name  (1)
PF02531 : PsaD
(13)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(13)
 
Diffraction radiation source type  (1)
Synchrotron
(13)
 
Diffraction source  (6)
ESRF BEAMLINE ID23-2
(5)
SLS BEAMLINE X06DA
(3)
ESRF BEAMLINE ID29
(2)
ESRF BEAMLINE ID2
(1)
SLS BEAMLINE X06SA
(1)
SPRING-8 BEAMLINE BL41XU
(1)
 
Synchrotron site  (3)
ESRF
(8)
SLS
(4)
SPring-8
(1)
 
Diffraction detector type  (3)
CCD
(6)
Pixel
(5)
Image plate
(1)
 
Refinement software  (3)
PHENIX
(7)
REFMAC
(6)
CNS
(1)
 
Representative Structures
Representative Structures
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Entries 1 to 10 of 13
Entries 1 to 10 of 13
 Select all entries on this page
Improved Model of Plant Photosystem I
Amunts A, Toporik H, Borovikov A, Nelson N
J Biol Chem (2010) [PMID: 19923216  ]
Assembly composition: protein/protein complex
Bound ligands: LMU    LMU    PQN    PQN    BCR    BCR    CLA    LMG    LMG   
Carbohydrate polymer components:
Molecule 1 - FRU(1), GLC(1)
Assembly name: Photosystem I (Preferred)   search this complex
PDBe complex ID: PDB-CPX-111633 (Preferred)   search this ID
PDBe-KB: P12353    P36886    Q9SQL2    P10793    P12357    P17227    (view 11 more)
X-ray diffraction
3.49Å resolution
Released: 17 Nov 2009
Model geometry
Fit model/data
2wse
2wse
2wse
The Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution
Amunts A, Drory O, Nelson N
Nature (2007) [PMID: 17476261  ]
Assembly composition: protein/protein complex
Bound ligands: PQN    PQN    BCR    BCR    CLA   
Assembly name: Photosystem I (Preferred)   search this complex
PDBe complex ID: PDB-CPX-138625 (Preferred)   search this ID
PDBe-KB: P12353    Q9SY97    Q9SQL2    P10793    P12357    P17227    (view 10 more)
X-ray diffraction
3.4Å resolution
Released: 8 May 2007
Model geometry
Fit model/data
2o01
2o01
2o01
Structure of synechocystis photosystem I trimer at 2.5A resolution
Nelson N, Malavath T, Caspy I
Biochim Biophys Acta Bioenerg (2018) [PMID: 29414678  ]
Assembly composition: protein/protein complex
Bound ligands: PQN    LMT    ZEX    ECH    ECH    MG    PQN    LHG    ACT    CA    EQ3    SQD    BCR    SQD    CA    45D    BCR    ZEX    CLA    CL    MG    EQ3    LMG    LMG    DGD    LHG    45D    DGD    LMT    ACT   
Assembly name: Photosystem I (Preferred)   search this complex
PDBe complex ID: PDB-CPX-146409 (Preferred)   search this ID
PDBe-KB: P19569    P37277    P29254    P32422    P29256    P72986    (view 5 more)
X-ray diffraction
2.501Å resolution
Released: 21 Feb 2018
Model geometry
Fit model/data
5oy0
5oy0
5oy0
The structure of plant photosystem I super-complex at 2.6 angstrom resolution.
Mazor Y, Borovikova A, Caspy I, Nelson N
Nat Plants (2017) [PMID: 28248295  ]
Source organism: Pisum sativum  
Assembly composition: protein/protein complex
Bound ligands: PQN    LMT    LUT    ZEX    PQN    XAT    LHG    CA    XAT    BCR    LUT    CA    BCR    ZEX    CLA    LMG    LMG    DGD    LHG    DGD    LMT   
Assembly name: Photosystem I (Preferred)   search this complex
PDBe complex ID: PDB-CPX-101280 (Preferred)   search this ID
PDBe-KB: E1C9K8    Q32904    E1C9K6    A0A0M3KL12    A0A0M3KL10    Q9SQL2    (view 10 more)
X-ray diffraction
2.6Å resolution
Released: 15 Mar 2017
Model geometry
Fit model/data
5l8r
5l8r
5l8r
Crystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC 6803
Mazor Y, Nataf D, Toporik H, Nelson N
Elife (2013) [PMID: 24473073  ]
Assembly composition: protein/protein complex
Bound ligands: PQN    PQN    LHG    BCR    BCR    CLA    LMG    LMG    LHG   
PDBe complex ID: PDB-CPX-146410 (Preferred)   search this ID
PDBe-KB: P19569    P29254    P32422    P29256    P37277    P72986    (view 5 more)
X-ray diffraction
3.8Å resolution
Released: 5 Feb 2014
Model geometry
Fit model/data
4l6v
4l6v
4l6v
Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution
Suga M, Qin X, Kuang T, Shen JR
Science (2015) [PMID: 26023133  ]
Source organism: Pisum sativum  
Assembly composition: protein/protein complex
Bound ligands: PQN    LMT    LUT    PQN    XAT    LHG    XAT    BCR    LUT    HTG    HTG    BCR    CLA    LMG    LMG    DGD    LHG    DGD    LMT   
Assembly name: Photosystem I (Preferred)   search this complex
PDBe complex ID: PDB-CPX-107293 (Preferred)   search this ID
PDBe-KB: A5Z2K3    Q32904    E1C9K6    C6T221    Q9SQL2    P10793    (view 10 more)
X-ray diffraction
2.8Å resolution
Released: 10 Jun 2015
Model geometry
Fit model/data
4xk8
4xk8
4xk8
Improved Model of Plant Photosystem I
Amunts A, Toporik H, Borovikov A, Nelson N
J Biol Chem (2010) [PMID: 19923216  ]
Assembly composition: protein/protein complex
Bound ligands: LMU    LMU    PQN    PQN    BCR    BCR    CLA    LMG    LMG   
Carbohydrate polymer components:
Molecule 1 - FRU(1), GLC(1)
Assembly name: Photosystem I (Preferred)   search this complex
PDBe complex ID: PDB-CPX-111632 (Preferred)   search this ID
PDBe-KB: P12353    P36886    Q9SQL2    P10793    P12357    P17227    (view 11 more)
X-ray diffraction
3.3Å resolution
Released: 17 Nov 2009
Model geometry
Fit model/data
2wsc
2wsc
2wsc
Improved model of plant photosystem I
Nelson N, Toporik H
J Biol Chem (2010) [PMID: 19923216  ]
Assembly composition: protein/protein complex
Bound ligands: LMU    LMU    PQN    PQN    BCR    BCR    CLA    LMG    LMG   
Assembly name: Photosystem I (Preferred)   search this complex
PDBe complex ID: PDB-CPX-122784 (Preferred)   search this ID
PDBe-KB: E1C9K8    Q32904    E1C9K6    Q9SQL2    P10793    P17227    (view 11 more)
X-ray diffraction
3.3Å resolution
Released: 18 Aug 2010
Model geometry
Fit model/data
3lw5
3lw5
3lw5
Crystal structure of plant Photosystem I at 3 Angstrom resolution
Mazor Y, Borovikova A, Greenberg I, Nelson N
To be published
Source organism: Pisum sativum  
Assembly composition: protein/protein complex
Bound ligands: PQN    LUT    G3P    PQN    LHG    BCR    LUT    NEX    G3P    BCR    CLA    LMG    LMG    DGD    LHG    DGD    NEX   
Assembly name: Photosystem I (Preferred)   search this complex
PDBe complex ID: PDB-CPX-101377 (Preferred)   search this ID
PDBe-KB: E1C9K8    Q32904    E1C9K6    Q9SQL2    P10793    P17227    (view 11 more)
X-ray diffraction
3Å resolution
Released: 4 Feb 2015
Model geometry
Fit model/data
4rku
4rku
4rku
Crystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC 6803
Mazor Y, Nataf D, Toporik H, Nelson N
Elife (2013) [PMID: 24473073  ]
Assembly composition: protein/protein complex
Bound ligands: LMU    LMU    PQN    PQN    LHG    BCR    BCR    CLA    CL    LMG    LMG    LHG   
Assembly name: Photosystem I (Preferred)   search this complex
PDBe complex ID: PDB-CPX-146412 (Preferred)   search this ID
PDBe-KB: P19569    P29254    P32422    P29256    P72986    P29255    (view 3 more)
X-ray diffraction
2.8Å resolution
Released: 5 Feb 2014
Model geometry
Fit model/data
4kt0
4kt0
4kt0
Entries 1 to 10 of 13
Entries 1 to 10 of 13