High-resolution structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803
External Resource: Annotation
- Domain Annotation: SCOP2 Classification
- Domain Annotation: ECOD Classification
- Domain Annotation: CATH
- Protein Family Annotation
- Gene Ontology: Gene Product Annotation
- InterPro: Protein Family Classification
- Membrane Protein Annotation: OPM
- Membrane Protein Annotation: PDBTM
- Membrane Protein Annotation: mpstruc
- Protein Modification Annotation
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| I [auth J] | SCOP2B Superfamily | Photosystem II reaction center protein J, PsbJ | 8106244 | 3001534 | SCOP2B (2022-06-29) |
| DA [auth j] | SCOP2B Superfamily | Photosystem II reaction center protein J, PsbJ | 8106244 | 3001534 | SCOP2B (2022-06-29) |
| H [auth I] | SCOP2B Superfamily | Photosystem II reaction center protein I, PsbI | 8099534 | 3001590 | SCOP2B (2022-06-29) |
| CA [auth i] | SCOP2B Superfamily | Photosystem II reaction center protein I, PsbI | 8099534 | 3001590 | SCOP2B (2022-06-29) |
| G [auth H] | SCOP2B Superfamily | Photosystem II 10 kDa phosphoprotein PsbH | 8098516 | 3001547 | SCOP2B (2022-06-29) |
| BA [auth h] | SCOP2B Superfamily | Photosystem II 10 kDa phosphoprotein PsbH | 8098516 | 3001547 | SCOP2B (2022-06-29) |
| F | SCOP2B Superfamily | Cytochrome b559 subunits | 8098318 | 3001602 | SCOP2B (2022-06-29) |
| AA [auth f] | SCOP2B Superfamily | Cytochrome b559 subunits | 8098318 | 3001602 | SCOP2B (2022-06-29) |
| Z [auth e] | SCOP2B Superfamily | Cytochrome b559 subunits | 8098316 | 3001602 | SCOP2B (2022-06-29) |
| E | SCOP2B Superfamily | Cytochrome b559 subunits | 8098316 | 3001602 | SCOP2B (2022-06-29) |
| Y [auth d] | SCOP2B Superfamily | Bacterial photosystem II reaction centre, L and M subunits | 8098320 | 3000736 | SCOP2B (2022-06-29) |
| D | SCOP2B Superfamily | Bacterial photosystem II reaction centre, L and M subunits | 8098320 | 3000736 | SCOP2B (2022-06-29) |
| X [auth c] | SCOP2B Superfamily | Photosystem II antenna protein-like | 8098322 | 3001674 | SCOP2B (2022-06-29) |
| C | SCOP2B Superfamily | Photosystem II antenna protein-like | 8098322 | 3001674 | SCOP2B (2022-06-29) |
| U [auth Z] | SCOP2B Superfamily | PsbZ-like | 8106246 | 3001624 | SCOP2B (2022-06-29) |
| PA [auth z] | SCOP2B Superfamily | PsbZ-like | 8106246 | 3001624 | SCOP2B (2022-06-29) |
| W [auth b] | SCOP2B Superfamily | Photosystem II antenna protein-like | 8098282 | 3001674 | SCOP2B (2022-06-29) |
| B | SCOP2B Superfamily | Photosystem II antenna protein-like | 8098282 | 3001674 | SCOP2B (2022-06-29) |
| R [auth V] | SCOP2B Superfamily | Cytochrome c | 8032498 | 3000815 | SCOP2B (2022-06-29) |
| MA [auth v] | SCOP2B Superfamily | Cytochrome c | 8032498 | 3000815 | SCOP2B (2022-06-29) |
| Q [auth U] | SCOP2B Superfamily | PsbU/PolX domain-like | 8106294 | 3000893 | SCOP2B (2022-06-29) |
| LA [auth u] | SCOP2B Superfamily | PsbU/PolX domain-like | 8106294 | 3000893 | SCOP2B (2022-06-29) |
| M [auth O] | SCOP2B Superfamily | OMPA barrel-like | 8106230 | 3000208 | SCOP2B (2022-06-29) |
| HA [auth o] | SCOP2B Superfamily | OMPA barrel-like | 8106230 | 3000208 | SCOP2B (2022-06-29) |
| L [auth M] | SCOP2B Superfamily | Photosystem II reaction center protein M, PsbM | 8101579 | 3001573 | SCOP2B (2022-06-29) |
| GA [auth m] | SCOP2B Superfamily | Photosystem II reaction center protein M, PsbM | 8101579 | 3001573 | SCOP2B (2022-06-29) |
| K [auth L] | SCOP2B Superfamily | Photosystem II reaction center protein L, PsbL | 8099538 | 3001523 | SCOP2B (2022-06-29) |
| FA [auth l] | SCOP2B Superfamily | Photosystem II reaction center protein L, PsbL | 8099538 | 3001523 | SCOP2B (2022-06-29) |
| J [auth K] | SCOP2B Superfamily | Photosystem II reaction center protein K, PsbK | 8098520 | 3001585 | SCOP2B (2022-06-29) |
| EA [auth k] | SCOP2B Superfamily | Photosystem II reaction center protein K, PsbK | 8098520 | 3001585 | SCOP2B (2022-06-29) |
| V [auth a] | SCOP2B Superfamily | Bacterial photosystem II reaction centre, L and M subunits | 8098522 | 3000736 | SCOP2B (2022-06-29) |
| A | SCOP2B Superfamily | Bacterial photosystem II reaction centre, L and M subunits | 8098522 | 3000736 | 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) |
|---|---|---|---|---|---|---|---|---|
| I [auth J] | PsbJ | e7n8oJ1 | 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) |
| DA [auth j] | PsbJ | e7n8oj1 | 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) |
| H [auth I] | PsbI | e7n8oI1 | 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) |
| CA [auth i] | PsbI | e7n8oi1 | 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) |
| G [auth H] | PsbH | e7n8oH1 | 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 h] | PsbH | e7n8oh1 | 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) |
| F | Cytochrom_B559 | e7n8oF1 | 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) |
| AA [auth f] | Cytochrom_B559 | e7n8of1 | 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 e] | Cytochrom_B559a | e7n8oe1 | 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) |
| E | Cytochrom_B559a | e7n8oE1 | 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 d] | Photo_RC | e7n8od1 | 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) |
| D | Photo_RC | e7n8oD1 | 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 c] | PSII_1st | e7n8oc1 | 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) |
| C | PSII_1st | e7n8oC1 | 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) |
| U [auth Z] | Ycf9 | e7n8oZ1 | A: extended segments | X: PsbZ-like (From Topology) | H: PsbZ-like (From Topology) | T: PsbZ-like | F: Ycf9 | ECOD (1.6) |
| PA [auth z] | Ycf9 | e7n8oz1 | A: extended segments | X: PsbZ-like (From Topology) | H: PsbZ-like (From Topology) | T: PsbZ-like | F: Ycf9 | ECOD (1.6) |
| T [auth Y] | PSII_Ycf12 | e7n8oY1 | 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) |
| OA [auth y] | PSII_Ycf12 | e7n8oy1 | 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) |
| W [auth b] | PSII_1st | e7n8ob1 | 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 b] | PSII_2nd | e7n8ob2 | 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) |
| B | PSII_1st | e7n8oB1 | 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 | e7n8oB2 | 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) |
| NA [auth x] | PsbX | e7n8ox1 | 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) |
| S [auth X] | PsbX | e7n8oX1 | 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 V] | Cytochrom_C550 | e7n8oV1 | A: alpha arrays | X: Cytochrome c-like | H: Cytochrome c (From Topology) | T: Cytochrome c | F: Cytochrom_C550 | ECOD (1.6) |
| MA [auth v] | Cytochrom_C550 | e7n8ov1 | A: alpha arrays | X: Cytochrome c-like | H: Cytochrome c (From Topology) | T: Cytochrome c | F: Cytochrom_C550 | ECOD (1.6) |
| Q [auth U] | PsbU | e7n8oU1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: PsbU | ECOD (1.6) |
| LA [auth u] | PsbU | e7n8ou1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: PsbU | ECOD (1.6) |
| P [auth T] | F_UNCLASSIFIED | e7n8oT1 | 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: F_UNCLASSIFIED | ECOD (1.6) |
| KA [auth t] | F_UNCLASSIFIED | e7n8ot1 | 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: F_UNCLASSIFIED | ECOD (1.6) |
| O [auth R] | PsbY | e7n8oR1 | 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) |
| JA [auth r] | PsbY | e7n8or1 | 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) |
| N [auth Q] | PsbQ_1 | e7n8oQ1 | A: alpha bundles | X: Four-helical up-and-down bundle | H: Oxygen-evolving enhancer protein 3 (From Topology) | T: Oxygen-evolving enhancer protein 3 | F: PsbQ_1 | ECOD (1.6) |
| IA [auth q] | PsbQ_1 | e7n8oq1 | A: alpha bundles | X: Four-helical up-and-down bundle | H: Oxygen-evolving enhancer protein 3 (From Topology) | T: Oxygen-evolving enhancer protein 3 | F: PsbQ_1 | ECOD (1.6) |
| M [auth O] | MSP | e7n8oO1 | A: beta barrels | X: Outer membrane meander beta-barrels | H: OMPA-like (From Topology) | T: OMPA-like | F: MSP | ECOD (1.6) |
| HA [auth o] | MSP | e7n8oo1 | A: beta barrels | X: Outer membrane meander beta-barrels | H: OMPA-like (From Topology) | T: OMPA-like | F: MSP | ECOD (1.6) |
| L [auth M] | PsbM | e7n8oM1 | 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) |
| GA [auth m] | PsbM | e7n8om1 | 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) |
| K [auth L] | PsbL | e7n8oL1 | 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 l] | PsbL | e7n8ol1 | 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) |
| J [auth K] | PsbK | e7n8oK1 | 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 k] | PsbK | e7n8ok1 | 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) |
| V [auth a] | Photo_RC | e7n8oa1 | 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) |
| A | Photo_RC | e7n8oA1 | 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) |
Domain Annotation: CATH CATH Database Homepage
| Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
|---|---|---|---|---|---|---|
| Z [auth e] | 1.20.5.860 | Mainly Alpha | Up-down Bundle | Single alpha-helices involved in coiled-coils or other helix-helix interfaces | Photosystem II cytochrome b559, alpha subunit | CATH (utative) |
| E | 1.20.5.860 | Mainly Alpha | Up-down Bundle | Single alpha-helices involved in coiled-coils or other helix-helix interfaces | Photosystem II cytochrome b559, alpha subunit | CATH (utative) |
| V [auth a] | 1.20.85.10 | Mainly Alpha | Up-down Bundle | Photosynthetic Reaction Center, subunit M | domain 1 | CATH (utative) |
| A | 1.20.85.10 | Mainly Alpha | Up-down Bundle | Photosynthetic Reaction Center, subunit M | domain 1 | CATH (utative) |
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 |
Membrane Protein Annotation: PDBTM PDBTM Database Homepage
| Chains | External Link | Comment |
|---|---|---|
| PDBTM | Annotated as membrane protein by PDBTM |
Membrane Protein Annotation: mpstruc mpstruc Database Homepage
| Chains | Resource Link | Group | Subgroup | Protein |
|---|---|---|---|---|
| mpstruc | TRANSMEMBRANE PROTEINS: ALPHA-HELICAL | Photosystems | Photosystem II, full electron dose |
Protein Modification Annotation
| Modified Residue(s) | ||
|---|---|---|
| Chain | Residue(s) | Description |
| DA [auth j], I [auth J] | 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 |
| CA [auth i], H [auth I] | 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 |
| KA [auth t], P [auth T] | 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 |
| GA [auth m], L [auth M] | FME | Parent Component: MET :  AA0021 , AA0566 , 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 , 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 |














