All structure family : Photosystem II cytochrome b559, alpha subunit
 
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Entries released this week  (1)
revised
(1)
 
Entry Information
Entry status  (1)
REL
(28)
 
Experimental methods  (2)
X-ray diffraction
(25)
Electron Microscopy
(3)
 
Authors  (206)
Shen JR
(12)
Umena Y
(10)
Kern J
(8)
Zouni A
(8)
Akita F
(7)
Kamiya N
(7)
Nakajima Y
(7)
Suga M
(7)
Yamamoto M
(6)
Yamashita K
(6)
Dobbek H
(5)
Iwata S
(5)
Kawakami K
(5)
Noguchi T
(5)
Zhu D
(5)
Aquila A
(4)
Boutet S
(4)
Chatterjee R
(4)
Chen JH
(4)
Hatsui T
(4)
Hunter MS
(4)
Hussein R
(4)
Ibrahim M
(4)
Inoue S
(4)
Ishikawa T
(4)
Joti Y
(4)
Kameshima T
(4)
Kato Y
(4)
Kimura T
(4)
Koglin JE
(4)
Kubo M
(4)
Liang M
(4)
Masuda T
(4)
Matsuura Y
(4)
Motomura T
(4)
Naitow H
(4)
Nakabayashi M
(4)
Nakane T
(4)
Nakano T
(4)
Nango E
(4)
Nomura T
(4)
Nureki O
(4)
Sakamoto T
(4)
Sugahara M
(4)
Suzuki M
(4)
Tanaka R
(4)
Tono K
(4)
Yabashi M
(4)
Yamane T
(4)
Yamashita A
(4)
Yano J
(4)
Yonekura S
(4)
Yu LJ
(4)
Zhang M
(4)
Adams PD
(3)
Afonine PV
(3)
Aller P
(3)
Alonso-Mori R
(3)
Andi B
(3)
Bean MA
(3)
Bergmann U
(3)
Brauer P
(3)
Brewster AS
(3)
Brunger AT
(3)
Bräuer P
(3)
Cao P
(3)
Chang WR
(3)
Cheah MH
(3)
Docker PT
(3)
Douthit L
(3)
Evans G
(3)
Fransson T
(3)
Fuller F
(3)
Fuller FD
(3)
Glownia JM
(3)
Gul S
(3)
Koroidov S
(3)
Kroll T
(3)
Kubin M
(3)
Laksmono H
(3)
Lane TJ
(3)
Lassalle L
(3)
Li M
(3)
Liebschner D
(3)
Liu ZF
(3)
Long Vo P
(3)
Lyubimov AY
(3)
Messinger J
(3)
Michels-Clark T
(3)
Moriarty NW
(3)
Nelson S
(3)
Nilsson H
(3)
Orville AM
(3)
Pastor E
(3)
Robinson J
(3)
Saenger W
(3)
Saracini C
(3)
Sauter NK
(3)
Seuffert I
(3)
Shen J-R
(3)
 
More...
 
Homo / hetero assembly  (1)
hetero
(28)
 
Assembly composition  (1)
protein/protein complex
(28)
 
Assembly polymer count  (11)
icosamer
(7)
40-mer
(6)
38-mer
(5)
nonadecamer
(3)
36-mer
(1)
39-mer
(1)
50-mer
(1)
54-mer
(1)
56-mer
(1)
decamer
(1)
octadecamer
(1)
 
Resolution distribution
1.5 - 2
(6)
2.0 - 2.5
(10)
2.5 - 3
(3)
3.0 - 3.5
(6)
3.5 - 4
(3)
 
Release year distribution
2000 - 2005
(3)
2005 - 2010
(4)
2010 - 2015
(6)
2015 - 2020
(17)
 
Journal  (10)
Nature
(13)
Proc Natl Acad Sci U S A
(3)
Science
(3)
J Am Chem Soc
(2)
J Biol Chem
(2)
Chem Phys
(1)
Elife
(1)
Faraday Discuss
(1)
Photosynth Res
(1)
Structure
(1)
 
Macromolecules
Organism superkingdom  (2)
Bacteria
(25)
Eukaryota
(3)
 
Organism name  (5)
Thermostichus vulcanus
(13)
Thermosynechococcus vestitus BP-1
(9)
Thermosynechococcus vestitus
(3)
Pisum sativum
(2)
Spinacia oleracea
(1)
 
Molecule name  (2)
Cytochrome b559 subunit alpha
(28)
PSII reaction center subunit V
(28)
 
Molecule type  (1)
Protein
(28)
 
Gene names  (2)
psbE
(28)
tsr1541
(12)
 
Interacting Molecules  (38)
Cytochrome b559 subunit beta
(28)
Photosystem II CP43 reaction center protein
(28)
Photosystem II CP47 reaction center protein
(28)
Photosystem II D2 protein
(28)
Photosystem II reaction center protein H
(27)
Photosystem II reaction center protein I
(27)
Photosystem II reaction center protein J
(27)
Photosystem II reaction center protein K
(27)
Photosystem II reaction center protein L
(27)
Photosystem II reaction center protein T
(27)
Photosystem II reaction center protein Z
(27)
Photosystem II reaction center protein M
(26)
Photosystem II extrinsic protein V
(25)
Photosystem II extrinsic protein O
(24)
Photosystem II extrinsic protein U
(24)
Photosystem II reaction center protein X
(23)
Photosystem II reaction center protein Psb30
(22)
Photosystem II protein D1
(16)
Photosystem II reaction center protein Y
(14)
Photosystem II protein D1 1
(12)
Chlorophyll a-b binding protein, chloroplastic
(3)
Oxygen-evolving enhancer protein 1, chloroplastic
(3)
Chlorophyll a-b binding protein 8, chloroplastic
(2)
Oxygen-evolving enhancer protein 2, chloroplastic
(2)
PSII 6.1 kDa protein
(2)
Ultraviolet-B-repressible protein
(2)
Chlorophyll A-B Binding protein 26 kD (CP26)
(1)
Oxygen-evolving enhancer protein 3
(1)
Oxygen-evolving enhancer protein 3, chloroplastic
(1)
PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN
(1)
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE
(1)
Photosystem II PsbN protein
(1)
Photosystem II Reaction Center Tn protein
(1)
Photosystem II Reaction Center X protein
(1)
Photosystem II luminal extrinsic protein Tn, PsbTn
(1)
Photosystem II reaction center W protein, chloroplastic
(1)
UNASSIGNED SUBUNITS
(1)
Unassigned subunits
(1)
 
Interacting ligands  (14)
HEM : PROTOPORPHYRIN IX CONTAINING FE
(26)
LHG : 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
(17)
LMT : DODECYL-BETA-D-MALTOSIDE
(12)
DGD : DIGALACTOSYL DIACYL GLYCEROL (DGDG)
(10)
UNL : Unknown ligand
(5)
DMS : DIMETHYL SULFOXIDE
(4)
GOL : GLYCEROL
(4)
1PE : PENTAETHYLENE GLYCOL
(1)
EDO : 1,2-ETHANEDIOL
(1)
HEC : HEME C
(1)
HTG : heptyl 1-thio-beta-D-glucopyranoside
(1)
P6G : HEXAETHYLENE GLYCOL
(1)
PG4 : TETRAETHYLENE GLYCOL
(1)
PGE : TRIETHYLENE GLYCOL
(1)
 
Function and Biology
EC number / name  (1)
1.10.3.9 : Photosystem II
(1)
 
Biological function  (4)
electron transfer activity
(28)
heme binding
(28)
iron ion binding
(28)
metal ion binding
(28)
 
Biological process  (3)
photosynthesis
(28)
photosynthesis, light reaction
(28)
photosynthetic electron transport chain
(28)
 
Biological cell component  (10)
membrane
(28)
photosystem II
(28)
photosystem II reaction center
(28)
thylakoid
(28)
cytoplasm
(25)
plasma membrane-derived thylakoid membrane
(25)
thylakoid membrane
(25)
chloroplast
(3)
chloroplast thylakoid membrane
(3)
plastid
(3)
 
Compound cofactor class  (1)
Heme
(1)
 
Sequence and Structure classification
SCOP fold  (2)
Photosystems
(1)
Single transmembrane helix
(1)
 
SCOP family  (2)
Cytochrome b559 subunits
(1)
Photosystems
(1)
 
CATH class  (1)
Mainly Alpha
(28)
 
CATH topology  (1)
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(28)
 
Pfam accession / name  (2)
PF00283 : Cytochrom_B559
(28)
PF00284 : Cytochrom_B559a
(28)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(25)
 
Diffraction radiation source type  (2)
Synchrotron
(15)
Free-electron laser
(10)
 
Diffraction source  (12)
SACLA BEAMLINE BL3
(6)
SPRING-8 BEAMLINE BL44XU
(4)
SLAC LCLS BEAMLINE CXI
(3)
SPRING-8 BEAMLINE BL41XU
(3)
ESRF BEAMLINE ID14-2
(2)
SPRING-8 BEAMLINE BL38B1
(2)
BESSY BEAMLINE 14.1
(1)
ESRF BEAMLINE ID29
(1)
OTHER
(1)
SLAC LCLS BEAMLINE MFX
(1)
SLAC LCLS BEAMLINE XPP
(1)
SLS BEAMLINE X06SA
(1)
 
Synchrotron site  (7)
SPring-8
(9)
SACLA
(6)
SLAC LCLS
(4)
ESRF
(3)
BESSY
(1)
PETRA III, DESY
(1)
SLS
(1)
 
Diffraction detector type  (2)
CCD
(19)
Pixel
(6)
 
Refinement software  (3)
PHENIX
(14)
REFMAC
(7)
CNS
(6)
 
EM microscope model  (1)
FEI TITAN KRIOS
(3)
 
EM detector name  (2)
GATAN K2 SUMMIT (4k x 4k)
(2)
OTHER
(1)
 
Representative Structures
Representative Structures
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Entries 1 to 10 of 28
Entries 1 to 10 of 28
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Room temperature XFEL structure of the native, doubly-illuminated photosystem II complex
Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Pham LV, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng T-C, Pastor E, Weninger C, Fransson T, Lassalle L, Braeuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Watermann DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J
Nature (2016) [PMID: 27871088  ]
Assembly composition: protein/protein complex
Bound ligands: HEM    LHG    BCR    PL9    SQD    BCT    SQD    BCR    HEM    PL9    CL    CLA    HEC    DGD    FE2    LHG    LMG    LMG    DGD    FE2    PHO   
Modified residues: FME    FME   
Assembly name: Photosystem II (Preferred)   search this complex
PDBe complex ID: PDB-CPX-141186 (Preferred)   search this ID
PDBe-KB: Q8DIP0    Q8DIF8    Q8DJI1    Q8DIQ1    Q9F1K9    P0A444    (view 14 more)
X-ray diffraction
2.2500038Å resolution
Released: 23 Nov 2016
Model geometry
Fit model/data
5tis
5tis
5tis
Native XFEL structure of Photosystem II (preflash two-flash dataset
Suga M, Shen JR
Nature (2017) [PMID: 28219079  ]
Assembly composition: protein/protein complex
Bound ligands: HEM    LMT    CA    LHG    MG    BCR    GOL    PL9    SQD    BCT    CA    SQD    BCR    HEM    HTG    HTG    PL9    CL    CLA    HEC    MG    DGD    FE2    LHG    LMG    LMG    DGD    FE2    LMT    PHO   
Modified residues: FME    FME   
Assembly name: Photosystem II (Preferred)   search this complex
PDBe complex ID: PDB-CPX-112066 (Preferred)   search this ID
PDBe-KB: P12238    P19052    P56152    D0VWR1    D0VWR7    P19054    (view 14 more)
X-ray diffraction
2.35Å resolution
Released: 15 Mar 2017
Model geometry
Fit model/data
5ws6
5ws6
5ws6
Native XFEL structure of photosystem II (dark dataset)
Suga M, Shen JR
Nature (2017) [PMID: 28219079  ]
Assembly composition: protein/protein complex
Bound ligands: HEM    LMT    CA    LHG    MG    BCR    GOL    PL9    SQD    BCT    CA    SQD    BCR    HEM    HTG    HTG    PL9    CL    CLA    HEC    MG    DGD    FE2    LHG    LMG    LMG    DGD    FE2    LMT    PHO   
Modified residues: FME    FME   
Assembly name: Photosystem II (Preferred)   search this complex
PDBe complex ID: PDB-CPX-112066 (Preferred)   search this ID
PDBe-KB: P12238    P19052    P56152    D0VWR1    D0VWR7    P19054    (view 14 more)
X-ray diffraction
2.5Å resolution
Released: 15 Mar 2017
Model geometry
Fit model/data
5gth
5gth
5gth
Native XFEL structure of photosystem II (preflash dark dataset)
Suga M, Shen JR
Nature (2017) [PMID: 28219079  ]
Assembly composition: protein/protein complex
Bound ligands: HEM    LMT    CA    LHG    MG    BCR    GOL    PL9    SQD    BCT    CA    SQD    BCR    HEM    HTG    HTG    PL9    CL    CLA    HEC    MG    DGD    FE2    LHG    LMG    LMG    DGD    FE2    LMT    PHO   
Modified residues: FME    FME   
Assembly name: Photosystem II (Preferred)   search this complex
PDBe complex ID: PDB-CPX-112066 (Preferred)   search this ID
PDBe-KB: P12238    P19052    P56152    D0VWR1    D0VWR7    P19054    (view 14 more)
X-ray diffraction
2.35Å resolution
Released: 15 Mar 2017
Model geometry
Fit model/data
5ws5
5ws5
5ws5
Photosystem II depleted of the Mn4CaO5 cluster at 2.55 A resolution
Zhang M, Bommer M, Chatterjee R, Hussain R, Kern J, Yano J, Dau H, Dobbek H, Zouni A
Elife (2017) [PMID: 28718766  ]
Assembly composition: protein/protein complex
Bound ligands: HEM    LHG    BCR    PL9    SQD    BCT    SQD    BCR    FE    FE    HEM    PL9    CL    CLA    HEC    DGD    LFA    LHG    LMG    LMG    DGD    PHO   
Assembly name: Photosystem II (Preferred)   search this complex
PDBe complex ID: PDB-CPX-141173 (Preferred)   search this ID
PDBe-KB: Q8DIP0    Q8DIF8    Q8DJI1    Q8DIQ1    Q9F1K9    P0A444    (view 14 more)
X-ray diffraction
2.197Å resolution
Released: 2 Aug 2017
Model geometry
Fit model/data
5mx2
5mx2
5mx2
Structure of unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Su XD, Ma J, Wei XP, Cao P, Zhu DJ, Chang WR, Liu ZF, Zhang XZ, Li M
Science (2017) [PMID: 28839073  ]
Source organism: Pisum sativum  
Assembly composition: protein/protein complex
Bound ligands: HEM    LUT    LHG    XAT    BCR    LUT    NEX    PL9    SQD    XAT    BCT    SQD    BCR    HEM    PL9    CLA    DGD    FE2    LHG    LMG    LMG    DGD    FE2    NEX    PHO   
PDBe complex ID: PDB-CPX-236764 (Preferred)   search this ID
PDBe-KB: P13554    A0A2D0TCJ0    Q9XQR6    P14226    A0A2D0TCJ3    P06585    (view 16 more)
Electron Microscopy
3.2Å resolution
Released: 20 Sep 2017
Model geometry
Fit model/data
Data not analysed
5xnm
5xnm
5xnm
Macromolecular diffractive imaging using imperfect crystals
Ayyer K, Yefanov O, Oberthur D, Roy-Chowdhury S, Galli L, Mariani V, Basu S, Coe J, Conrad CE, Fromme R, Schaffer A, Dorner K, James D, Kupitz C, Metz M, Nelson G, Xavier PL, Beyerlein KR, Schmidt M, Sarrou I, Spence JCH, Weierstall U, White TA, Yang J-H, Zhao Y, Liang M, Aquila A, Hunter MS, Koglin JE, Boutet S, Fromme P, Barty A, Chapman HN
Nature (2016) [PMID: 26863980  ]
Assembly composition: protein/protein complex
Bound ligands: HEM    CA    LHG    MG    BCR    PL9    SQD    BCT    CA    SQD    BCR    HEM    PL9    CL    CLA    MG    DGD    FE2    LHG    LMG    LMG    DGD    FE2    PHO   
Assembly name: Photosystem II (Preferred)   search this complex
PDBe complex ID: PDB-CPX-141187 (Preferred)   search this ID
PDBe-KB: Q8DIP0    Q8DIF8    Q8DJI1    Q8DIQ1    Q9F1K9    P0A444    (view 13 more)
X-ray diffraction
3.5Å resolution
Released: 8 Feb 2017
Model geometry
Fit model/data
5e79
5e79
5e79
Crystal structure analysis of Photosystem II complex
Tanaka A, Fukushima Y, Kamiya N
J Am Chem Soc (2017) [PMID: 28102667  ]
Assembly composition: protein/protein complex
Bound ligands: HEM    LMT    CA    LHG    MG    BCR    PL9    RRX    SQD    BCT    CA    DMS    SQD    BCR    DMS    HEM    HTG    HTG    PL9    CL    CLA    HEC    MG    DGD    FE2    LHG    LMG    LMG    DGD    FE2    LMT    PHO    RRX   
Modified residues: FME    FME   
Assembly name: Photosystem II (Preferred)   search this complex
PDBe complex ID: PDB-CPX-112074 (Preferred)   search this ID
PDBe-KB: P12238    P19052    P56152    D0VWR1    D0VWR7    P19054    (view 13 more)
X-ray diffraction
1.87Å resolution
Released: 1 Feb 2017
Model geometry
Fit model/data
5b5e
5b5e
5b5e
RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX
Wang J, Wiwczar JM, Brudvig GW
Photosynth Res (2017) [PMID: 28741056  ]
Assembly composition: protein/protein complex
Bound ligands: 2PE    HEM    LMT    P6G    CA    LHG    MG    P6G    PG4    BCR    GOL    PL9    SQD    BCT    CA    PE8    SQD    BCR    HEM    HTG    HTG    PL9    1PE    CL    CLA    HEC    MG    PG4    1PE    DGD    EDO    FE2    LHG    LMG    LMG    2PE    DGD    FE2    LMT    PE8    PGE    PGE    PHO   
Modified residues: FME    MHS    FME    MHS   
Assembly name: Photosystem II (Preferred)   search this complex
PDBe complex ID: PDB-CPX-112074 (Preferred)   search this ID
PDBe-KB: P12238    P19052    P56152    D0VWR1    D0VWR7    P19054    (view 13 more)
X-ray diffraction
1.9Å resolution
Released: 30 Aug 2017
Model geometry
Fit model/data
5v2c
5v2c
5v2c
Crystal structure of the PsbM-deletion mutant of photosystem II
Uto S, Kawakami K, Umena Y, Iwai M, Ikeuchi M, Shen JR, Kamiya N
Faraday Discuss (2017) [PMID: 28272640  ]
Assembly composition: protein/protein complex
Bound ligands: HEM    LMT    CA    LHG    MG    BCR    PL9    RRX    SQD    BCT    CA    DMS    SQD    BCR    DMS    HEM    HTG    HTG    PL9    CL    CLA    HEC    MG    DGD    FE2    LHG    LMG    LMG    DGD    FE2    LMT    PHO    RRX   
Modified residues: FME    FME   
Assembly name: Photosystem II (Preferred)   search this complex
PDBe complex ID: PDB-CPX-141175 (Preferred)   search this ID
PDBe-KB: Q8DIP0    Q8DIF8    Q8DJI1    Q8DIQ1    Q9F1K9    P0A444    (view 12 more)
X-ray diffraction
2.2Å resolution
Released: 22 Mar 2017
Model geometry
Fit model/data
5h2f
5h2f
5h2f
Entries 1 to 10 of 28
Entries 1 to 10 of 28