Brand  (β version)

PDB ID: 6DHF

Hetero Atom Contents

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Ligands
Code Name Style Show Link
BCR Beta-carotene PoSSuM
BCT Bicarbonate ion PoSSuM
CL Chloride ion PoSSuM
CLA Chlorophyll a PoSSuM
FE2 Fe (II) ion PoSSuM
HEC Heme C PoSSuM
HEM Protoporphyrin ix containing Fe PoSSuM
LHG 1,2-dipalmitoyl-phosphatidyl-glycerole PoSSuM
LMG 1,2-distearoyl-monogalactosyl-diglyceride PoSSuM
OEX Ca-mn4-o5 cluster PoSSuM
PHO Pheophytin a PoSSuM
PL9 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone PoSSuM
SQD 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol PoSSuM
UNL Unknown ligand PoSSuM
DGD Digalactosyl diacyl glycerol (dgdg) PoSSuM
Non-standard Residues
Code Name Show
FME N-formylmethionine
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 6DHF   PDBj   RCSB PDB   PDBe
Header : PHOTOSYNTHESIS
Title : RT XFEL structure of the one-flash state of Photosystem II (1F, S2-rich) at 2.08 Angstrom resolution
Release Data : 2018-11-21
Compound :
mol_id molecule chains synonym
1 Photosystem II protein D1 1 A,a PSII D1 protein 1,Photosystem II Q(B) protein 1
ec: 1.10.3.9
mol_id molecule chains synonym
2 Photosystem II CP47 reaction center protein B,b PSII 47 kDa protein,Protein CP-47
mol_id molecule chains synonym
3 Photosystem II CP43 reaction center protein C,c PSII 43 kDa protein,Protein CP-43
mol_id molecule chains synonym
4 Photosystem II D2 protein D,d PSII D2 protein,Photosystem II Q(A) protein
ec: 1.10.3.9
mol_id molecule chains synonym
5 Cytochrome b559 subunit alpha E,e PSII reaction center subunit V
mol_id molecule chains synonym
6 Cytochrome b559 subunit beta F,f PSII reaction center subunit VI
mol_id molecule chains synonym
7 Photosystem II reaction center protein H H,h PSII-H
mol_id molecule chains synonym
8 Photosystem II reaction center protein I I,i PSII-I,PSII 4.4 kDa protein
mol_id molecule chains synonym
9 Photosystem II reaction center protein J J,j PSII-J
mol_id molecule chains synonym
10 Photosystem II reaction center protein K K,k PSII-K
mol_id molecule chains synonym
11 Photosystem II reaction center protein L L,l PSII-L
mol_id molecule chains synonym
12 Photosystem II reaction center protein M M,m PSII-M
mol_id molecule chains synonym
13 Photosystem II manganese-stabilizing polypeptide O,o MSP
mol_id molecule chains synonym
14 Photosystem II reaction center protein T T,t PSII-Tc
mol_id molecule chains synonym
15 Photosystem II 12 kDa extrinsic protein U,u PS II complex 12 kDa extrinsic protein,PSII-U
mol_id molecule chains synonym
16 Cytochrome c-550 V,v Cytochrome c-549,Cytochrome c550,Low-potential cytochrome c
mol_id molecule chains
17 Photosystem II reaction center protein Ycf12 Y,y
mol_id molecule chains
18 Photosystem II reaction center X protein X,x
mol_id molecule chains synonym
19 Photosystem II reaction center protein Z Z,z PSII-Z
mol_id molecule chains
20 Photosystem II protein Y R,r
Source :
mol_id organism_scientific
1 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
2 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
3 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
4 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
5 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
6 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
7 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
8 Thermosynechococcus elongatus  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
9 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
10 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
11 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
12 Thermosynechococcus elongatus  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
13 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
14 Thermosynechococcus elongatus  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
15 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
16 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
17 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
18 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
19 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
mol_id organism_scientific
20 Thermosynechococcus elongatus (strain BP-1)  (taxid:197221)
strain: BP-1
other_details: cell
Authors : Kern, J., Chatterjee, R., Young, I.D., Fuller, F.D., Lassalle, L., Ibrahim, M., Gul, S., Fransson, T., Brewster, A.S., Alonso-Mori, R., Hussein, R., Zhang, M., Douthit, L., de Lichtenberg, C., Cheah, M.H., Shevela, D., Wersig, J., Seufert, I., Sokaras, D., Pastor, E., Weninger, C., Kroll, T., Sierra, R.G., Aller, P., Butryn, A., Orville, A.M., Liang, M., Batyuk, A., Koglin, J.E., Carbajo, S., Boutet, S., Moriarty, N.W., Holton, J.M., Dobbek, H., Adams, P.D., Bergmann, U., Sauter, N.K., Zouni, A., Messinger, J., Yano, J., Yachandra, V.K.
Keywords : PHOTOSYSTEMS, TRANSMEMBRANE, ROOM TEMPERATURE, ELECTRON TRANSPORT, PHOTOSYNTHESIS
Exp. method : X-RAY DIFFRACTION ( 2.0800 Å )
Citation :

Structures of the intermediates of Kok's photosynthetic water oxidation clock.

Kern, J.,Chatterjee, R.,Young, I.D.  et al.
(2018)  Nature  563 : 421 - 425

PubMed: 30405241
DOI: 10.1038/s41586-018-0681-2

Reaction

Chain : A, a
UniProt : P0A444 (PSBA1_THEVB)
Reaction: EC: Evidence:
Physiological Direction:
2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2 1.10.3.9 HAMAP-Rule:MF_01379, PubMed:20558739, PubMed:25006873
-
Chain : B, b
UniProt : Q8DIQ1 (PSBB_THEVB)
Reaction : -
Chain : C, c
UniProt : Q8DIF8 (PSBC_THEVB)
Reaction : -
Chain : D, d
UniProt : Q8CM25 (PSBD_THEVB)
Reaction: EC: Evidence:
Physiological Direction:
2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2 1.10.3.9 HAMAP-Rule:MF_01383, PubMed:20558739, PubMed:25006873
-
Chain : E, e
UniProt : Q8DIP0 (PSBE_THEVB)
Reaction : -
Chain : F, f
UniProt : Q8DIN9 (PSBF_THEVB)
Reaction : -
Chain : H, h
UniProt : Q8DJ43 (PSBH_THEVB)
Reaction : -
Chain : I, i
UniProt : Q8DJZ6 (PSBI_THEVB)
Reaction : -
Chain : J, j
UniProt : P59087 (PSBJ_THEVB)
Reaction : -
Chain : K, k
UniProt : Q9F1K9 (PSBK_THEVB)
Reaction : -
Chain : L, l
UniProt : Q8DIN8 (PSBL_THEVB)
Reaction : -
Chain : M, m
UniProt : Q8DHA7 (PSBM_THEVB)
Reaction : -
Chain : O, o
UniProt : P0A431 (PSBO_THEVB)
Reaction : -
Chain : T, t
UniProt : Q8DIQ0 (PSBT_THEVB)
Reaction : -
Chain : U, u
UniProt : Q9F1L5 (PSBU_THEVB)
Reaction : -
Chain : V, v
UniProt : P0A386 (CY550_THEVB)
Reaction : -
Chain : Y, y
UniProt : Q8DJI1 (PSB30_THEVB)
Reaction : -
Chain : X, x
UniProt : Q9F1R6 (PSBX_THEVB)
Reaction : -
Chain : Z, z
UniProt : Q8DHJ2 (PSBZ_THEVB)
Reaction : -
Chain : R, r
UniProt : Q8DKM3 (PSBY_THEVB)
Reaction : -