6DHE
RT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.05 Angstrom resolution
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
B | SCOP2B Superfamily | Photosystem II antenna protein-like | 8032743 | 3001674 | SCOP2B (2022-06-29) |
V [auth b] | SCOP2B Superfamily | Photosystem II antenna protein-like | 8032743 | 3001674 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Cytochrome b559 subunits | 8032749 | 3001602 | SCOP2B (2022-06-29) |
Y [auth e] | SCOP2B Superfamily | Cytochrome b559 subunits | 8032749 | 3001602 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Cytochrome b559 subunits | 8032752 | 3001602 | SCOP2B (2022-06-29) |
Z [auth f] | SCOP2B Superfamily | Cytochrome b559 subunits | 8032752 | 3001602 | SCOP2B (2022-06-29) |
CA [auth j] | SCOP2B Superfamily | Photosystem II reaction center protein J, PsbJ | 8032755 | 3001534 | SCOP2B (2022-06-29) |
I [auth J] | SCOP2B Superfamily | Photosystem II reaction center protein J, PsbJ | 8032755 | 3001534 | SCOP2B (2022-06-29) |
GA [auth o] | SCOP2B Superfamily | OMPA barrel-like | 8032765 | 3000208 | SCOP2B (2022-06-29) |
M [auth O] | SCOP2B Superfamily | OMPA barrel-like | 8032765 | 3000208 | SCOP2B (2022-06-29) |
HA [auth t] | SCOP2B Superfamily | Photosystem II reaction center protein T, PsbT | 8032769 | 3001561 | SCOP2B (2022-06-29) |
N [auth T] | SCOP2B Superfamily | Photosystem II reaction center protein T, PsbT | 8032769 | 3001561 | SCOP2B (2022-06-29) |
KA [auth y] | SCOP2B Superfamily | Photosystem II reaction center protein Ycf12 | 8093136 | 3002680 | SCOP2B (2022-06-29) |
Q [auth Y] | SCOP2B Superfamily | Photosystem II reaction center protein Ycf12 | 8093136 | 3002680 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Bacterial photosystem II reaction centre, L and M subunits | 8032741 | 3000736 | SCOP2B (2022-06-29) |
U [auth a] | SCOP2B Superfamily | Bacterial photosystem II reaction centre, L and M subunits | 8032741 | 3000736 | SCOP2B (2022-06-29) |
DA [auth k] | SCOP2B Superfamily | Photosystem II reaction center protein K, PsbK | 8032757 | 3001585 | SCOP2B (2022-06-29) |
J [auth K] | SCOP2B Superfamily | Photosystem II reaction center protein K, PsbK | 8032757 | 3001585 | SCOP2B (2022-06-29) |
EA [auth l] | SCOP2B Superfamily | Photosystem II reaction center protein L, PsbL | 8032759 | 3001523 | SCOP2B (2022-06-29) |
K [auth L] | SCOP2B Superfamily | Photosystem II reaction center protein L, PsbL | 8032759 | 3001523 | SCOP2B (2022-06-29) |
FA [auth m] | SCOP2B Superfamily | Photosystem II reaction center protein M, PsbM | 8032762 | 3001573 | SCOP2B (2022-06-29) |
L [auth M] | SCOP2B Superfamily | Photosystem II reaction center protein M, PsbM | 8032762 | 3001573 | SCOP2B (2022-06-29) |
IA [auth u] | SCOP2B Superfamily | PsbU/PolX domain-like | 8032768 | 3000893 | SCOP2B (2022-06-29) |
O [auth U] | SCOP2B Superfamily | PsbU/PolX domain-like | 8032768 | 3000893 | SCOP2B (2022-06-29) |
JA [auth v] | SCOP2B Superfamily | Cytochrome c | 8036565 | 3000815 | SCOP2B (2022-06-29) |
P [auth V] | SCOP2B Superfamily | Cytochrome c | 8036565 | 3000815 | SCOP2B (2022-06-29) |
MA [auth z] | SCOP2B Superfamily | PsbZ-like | 8032770 | 3001624 | SCOP2B (2022-06-29) |
S [auth Z] | SCOP2B Superfamily | PsbZ-like | 8032770 | 3001624 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Photosystem II antenna protein-like | 8032746 | 3001674 | SCOP2B (2022-06-29) |
W [auth c] | SCOP2B Superfamily | Photosystem II antenna protein-like | 8032746 | 3001674 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Bacterial photosystem II reaction centre, L and M subunits | 8032750 | 3000736 | SCOP2B (2022-06-29) |
X [auth d] | SCOP2B Superfamily | Bacterial photosystem II reaction centre, L and M subunits | 8032750 | 3000736 | SCOP2B (2022-06-29) |
AA [auth h] | SCOP2B Superfamily | Photosystem II 10 kDa phosphoprotein PsbH | 8032753 | 3001547 | SCOP2B (2022-06-29) |
G [auth H] | SCOP2B Superfamily | Photosystem II 10 kDa phosphoprotein PsbH | 8032753 | 3001547 | SCOP2B (2022-06-29) |
BA [auth i] | SCOP2B Superfamily | Photosystem II reaction center protein I, PsbI | 8032754 | 3001590 | SCOP2B (2022-06-29) |
H [auth I] | SCOP2B Superfamily | Photosystem II reaction center protein I, PsbI | 8032754 | 3001590 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | PSII_1st | e6dheB2 | A: alpha bundles | X: Photosystem II antenna protein-like (From Topology) | H: Photosystem II antenna protein-like (From Topology) | T: Photosystem II antenna protein-like | F: PSII_1st | ECOD (1.6) |
B | PSII_2nd | e6dheB1 | A: a+b two layers | X: Photosystem II antenna protein PsbB insertion domain (From Topology) | H: Photosystem II antenna protein PsbB insertion domain (From Topology) | T: Photosystem II antenna protein PsbB insertion domain | F: PSII_2nd | ECOD (1.6) |
V [auth b] | PSII_1st | e6dheb1 | A: alpha bundles | X: Photosystem II antenna protein-like (From Topology) | H: Photosystem II antenna protein-like (From Topology) | T: Photosystem II antenna protein-like | F: PSII_1st | ECOD (1.6) |
V [auth b] | PSII_2nd | e6dheb2 | A: a+b two layers | X: Photosystem II antenna protein PsbB insertion domain (From Topology) | H: Photosystem II antenna protein PsbB insertion domain (From Topology) | T: Photosystem II antenna protein PsbB insertion domain | F: PSII_2nd | ECOD (1.6) |
E | Cytochrom_B559a | e6dheE1 | A: extended segments | X: Cytochrome b559 subunits (From Topology) | H: Cytochrome b559 subunits (From Topology) | T: Cytochrome b559 subunits | F: Cytochrom_B559a | ECOD (1.6) |
Y [auth e] | Cytochrom_B559a | e6dhee1 | A: extended segments | X: Cytochrome b559 subunits (From Topology) | H: Cytochrome b559 subunits (From Topology) | T: Cytochrome b559 subunits | F: Cytochrom_B559a | ECOD (1.6) |
F | Cytochrom_B559 | e6dheF1 | A: extended segments | X: Cytochrome b559 subunits (From Topology) | H: Cytochrome b559 subunits (From Topology) | T: Cytochrome b559 subunits | F: Cytochrom_B559 | ECOD (1.6) |
Z [auth f] | Cytochrom_B559 | e6dhef1 | A: extended segments | X: Cytochrome b559 subunits (From Topology) | H: Cytochrome b559 subunits (From Topology) | T: Cytochrome b559 subunits | F: Cytochrom_B559 | ECOD (1.6) |
CA [auth j] | PsbJ | e6dhej1 | A: extended segments | X: Photosystem II reaction center protein J, PsbJ (From Topology) | H: Photosystem II reaction center protein J, PsbJ (From Topology) | T: Photosystem II reaction center protein J, PsbJ | F: PsbJ | ECOD (1.6) |
I [auth J] | PsbJ | e6dheJ1 | A: extended segments | X: Photosystem II reaction center protein J, PsbJ (From Topology) | H: Photosystem II reaction center protein J, PsbJ (From Topology) | T: Photosystem II reaction center protein J, PsbJ | F: PsbJ | ECOD (1.6) |
GA [auth o] | MSP | e6dheo1 | A: beta barrels | X: Outer membrane meander beta-barrels | H: OMPA-like (From Topology) | T: OMPA-like | F: MSP | ECOD (1.6) |
M [auth O] | MSP | e6dheO1 | A: beta barrels | X: Outer membrane meander beta-barrels | H: OMPA-like (From Topology) | T: OMPA-like | F: MSP | ECOD (1.6) |
HA [auth t] | PsbT | e6dhet1 | A: extended segments | X: Photosystem II reaction center protein T, PsbT (From Topology) | H: Photosystem II reaction center protein T, PsbT (From Topology) | T: Photosystem II reaction center protein T, PsbT | F: PsbT | ECOD (1.6) |
N [auth T] | PsbT | e6dheT1 | A: extended segments | X: Photosystem II reaction center protein T, PsbT (From Topology) | H: Photosystem II reaction center protein T, PsbT (From Topology) | T: Photosystem II reaction center protein T, PsbT | F: PsbT | ECOD (1.6) |
KA [auth y] | PSII_Ycf12 | e6dhey1 | A: extended segments | X: Photosystem II reaction center protein ycf12 (From Topology) | H: Photosystem II reaction center protein ycf12 (From Topology) | T: Photosystem II reaction center protein ycf12 | F: PSII_Ycf12 | ECOD (1.6) |
Q [auth Y] | PSII_Ycf12 | e6dheY1 | A: extended segments | X: Photosystem II reaction center protein ycf12 (From Topology) | H: Photosystem II reaction center protein ycf12 (From Topology) | T: Photosystem II reaction center protein ycf12 | F: PSII_Ycf12 | ECOD (1.6) |
LA [auth x] | PsbX | e6dhex1 | A: extended segments | X: Photosystem II PsbX protein (From Topology) | H: Photosystem II PsbX protein (From Topology) | T: Photosystem II PsbX protein | F: PsbX | ECOD (1.6) |
R [auth X] | PsbX | e6dheX1 | A: extended segments | X: Photosystem II PsbX protein (From Topology) | H: Photosystem II PsbX protein (From Topology) | T: Photosystem II PsbX protein | F: PsbX | ECOD (1.6) |
A | Photo_RC | e6dheA1 | A: alpha bundles | X: Bacterial photosystem II reaction centre L and M subunits-like (From Topology) | H: Bacterial photosystem II reaction centre L and M subunits-like (From Topology) | T: Bacterial photosystem II reaction centre L and M subunits-like | F: Photo_RC | ECOD (1.6) |
U [auth a] | Photo_RC | e6dhea1 | A: alpha bundles | X: Bacterial photosystem II reaction centre L and M subunits-like (From Topology) | H: Bacterial photosystem II reaction centre L and M subunits-like (From Topology) | T: Bacterial photosystem II reaction centre L and M subunits-like | F: Photo_RC | ECOD (1.6) |
DA [auth k] | PsbK | e6dhek1 | A: extended segments | X: Photosystem II reaction center protein K, PsbK (From Topology) | H: Photosystem II reaction center protein K, PsbK (From Topology) | T: Photosystem II reaction center protein K, PsbK | F: PsbK | ECOD (1.6) |
J [auth K] | PsbK | e6dheK1 | A: extended segments | X: Photosystem II reaction center protein K, PsbK (From Topology) | H: Photosystem II reaction center protein K, PsbK (From Topology) | T: Photosystem II reaction center protein K, PsbK | F: PsbK | ECOD (1.6) |
EA [auth l] | PsbL | e6dhel1 | A: extended segments | X: Photosystem II reaction center protein L, PsbL (From Topology) | H: Photosystem II reaction center protein L, PsbL (From Topology) | T: Photosystem II reaction center protein L, PsbL | F: PsbL | ECOD (1.6) |
K [auth L] | PsbL | e6dheL1 | A: extended segments | X: Photosystem II reaction center protein L, PsbL (From Topology) | H: Photosystem II reaction center protein L, PsbL (From Topology) | T: Photosystem II reaction center protein L, PsbL | F: PsbL | ECOD (1.6) |
FA [auth m] | PsbM | e6dhem1 | A: extended segments | X: Photosystem II reaction center protein M, PsbM (From Topology) | H: Photosystem II reaction center protein M, PsbM (From Topology) | T: Photosystem II reaction center protein M, PsbM | F: PsbM | ECOD (1.6) |
L [auth M] | PsbM | e6dheM1 | A: extended segments | X: Photosystem II reaction center protein M, PsbM (From Topology) | H: Photosystem II reaction center protein M, PsbM (From Topology) | T: Photosystem II reaction center protein M, PsbM | F: PsbM | ECOD (1.6) |
IA [auth u] | PsbU | e6dheu1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: PsbU | ECOD (1.6) |
O [auth U] | PsbU | e6dheU1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: PsbU | ECOD (1.6) |
JA [auth v] | Cytochrom_C550 | e6dhev1 | A: alpha arrays | X: Cytochrome c-like | H: Cytochrome c (From Topology) | T: Cytochrome c | F: Cytochrom_C550 | ECOD (1.6) |
P [auth V] | Cytochrom_C550 | e6dheV1 | A: alpha arrays | X: Cytochrome c-like | H: Cytochrome c (From Topology) | T: Cytochrome c | F: Cytochrom_C550 | ECOD (1.6) |
MA [auth z] | Ycf9 | e6dhez1 | A: extended segments | X: PsbZ-like (From Topology) | H: PsbZ-like (From Topology) | T: PsbZ-like | F: Ycf9 | ECOD (1.6) |
S [auth Z] | Ycf9 | e6dheZ1 | A: extended segments | X: PsbZ-like (From Topology) | H: PsbZ-like (From Topology) | T: PsbZ-like | F: Ycf9 | ECOD (1.6) |
NA [auth r] | PsbY | e6dher1 | A: extended segments | X: Photosystem II protein Y, psbY (From Topology) | H: Photosystem II protein Y, psbY (From Topology) | T: Photosystem II protein Y, psbY | F: PsbY | ECOD (1.6) |
T [auth R] | PsbY | e6dheR1 | A: extended segments | X: Photosystem II protein Y, psbY (From Topology) | H: Photosystem II protein Y, psbY (From Topology) | T: Photosystem II protein Y, psbY | F: PsbY | ECOD (1.6) |
C | PSII_1st | e6dheC1 | A: alpha bundles | X: Photosystem II antenna protein-like (From Topology) | H: Photosystem II antenna protein-like (From Topology) | T: Photosystem II antenna protein-like | F: PSII_1st | ECOD (1.6) |
W [auth c] | PSII_1st | e6dhec1 | A: alpha bundles | X: Photosystem II antenna protein-like (From Topology) | H: Photosystem II antenna protein-like (From Topology) | T: Photosystem II antenna protein-like | F: PSII_1st | ECOD (1.6) |
D | Photo_RC | e6dheD1 | A: alpha bundles | X: Bacterial photosystem II reaction centre L and M subunits-like (From Topology) | H: Bacterial photosystem II reaction centre L and M subunits-like (From Topology) | T: Bacterial photosystem II reaction centre L and M subunits-like | F: Photo_RC | ECOD (1.6) |
X [auth d] | Photo_RC | e6dhed1 | A: alpha bundles | X: Bacterial photosystem II reaction centre L and M subunits-like (From Topology) | H: Bacterial photosystem II reaction centre L and M subunits-like (From Topology) | T: Bacterial photosystem II reaction centre L and M subunits-like | F: Photo_RC | ECOD (1.6) |
AA [auth h] | PsbH | e6dheh1 | A: extended segments | X: Photosystem II 10 kDa phosphoprotein PsbH (From Topology) | H: Photosystem II 10 kDa phosphoprotein PsbH (From Topology) | T: Photosystem II 10 kDa phosphoprotein PsbH | F: PsbH | ECOD (1.6) |
G [auth H] | PsbH | e6dheH1 | A: extended segments | X: Photosystem II 10 kDa phosphoprotein PsbH (From Topology) | H: Photosystem II 10 kDa phosphoprotein PsbH (From Topology) | T: Photosystem II 10 kDa phosphoprotein PsbH | F: PsbH | ECOD (1.6) |
BA [auth i] | PsbI | e6dhei1 | A: extended segments | X: Photosystem II reaction center protein I, PsbI (From Topology) | H: Photosystem II reaction center protein I, PsbI (From Topology) | T: Photosystem II reaction center protein I, PsbI | F: PsbI | ECOD (1.6) |
H [auth I] | PsbI | e6dheI1 | A: extended segments | X: Photosystem II reaction center protein I, PsbI (From Topology) | H: Photosystem II reaction center protein I, PsbI (From Topology) | T: Photosystem II reaction center protein I, PsbI | F: PsbI | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Membrane Protein Annotation: OPM OPM Database Homepage
Chains | External Link | Type | Class | Superfamily | Family |
---|---|---|---|---|---|
OPM | Transmembrane | Alpha-helical polytopic | Photosystems | Photosystem II |
Protein Modification Annotation
Modified Residue(s) | ||
---|---|---|
Chain | Residue(s) | Description |
HA [auth t], N [auth T] | FME | Parent Component: MET :  AA0021 , AA0566 :  N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 |
FA [auth m], L [auth M] | FME | Parent Component: MET :  AA0021 , AA0566 , AA0021 , AA0566 :  N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 |
BA [auth i], H [auth I] | FME | Parent Component: MET :  AA0021 , AA0566 , AA0021 , AA0566 , AA0021 , AA0566 :  N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 |