Universal Photosystem II Intermediate with Light-Dependent Water-Ferrocyanide Oxydo-reductase activity from Chlamydomonas reinhardtii
Nelson, N., Klaiman, D., Fadeeva, M., Kandiah, E.To be published.
Experimental Data Snapshot
wwPDB Validation 3D Report Full Report
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II protein D1 | 334 | Chlamydomonas reinhardtii | Mutation(s): 0  EC: 1.10.3.9 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07753 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II CP47 reaction center protein | 480 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P37255 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein Psb30 | C [auth V] | 32 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P50370 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II CP43 reaction center protein | D [auth C] | 449 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P10898 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II D2 protein | E [auth D] | 348 | Chlamydomonas reinhardtii | Mutation(s): 0  EC: 1.10.3.9 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06007 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b559 subunit alpha | F [auth E] | 75 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P48268 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b559 subunit beta | G [auth F] | 31 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q08363 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein H | 66 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P22666 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein I | 34 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P59763 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 10 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein J | 36 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O19930 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 11 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein K | 37 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P18263 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 12 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein L | 35 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q1KVX2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 13 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein M | 29 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P92277 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 14 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Oxygen-evolving enhancer protein 1, chloroplastic | N [auth O] | 240 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P12853 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 15 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Oxygen-evolving enhancer protein 2, chloroplastic | O [auth P] | 188 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P11471 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 16 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Oxygen-evolving enhancer protein 3, chloroplastic | P [auth Q] | 148 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P12852 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 17 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein T | Q [auth T] | 30 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P37256 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 18 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 4.1 kDa photosystem II subunit | R [auth X] | 32 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A8I846 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 19 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein Z | S [auth Z] | 61 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P92276 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 20 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein U | T [auth U] | 23 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A8I5A0 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 21 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center W protein, chloroplastic | U [auth W] | 44 | Chlamydomonas reinhardtii | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9SPI9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
| Ligands 14 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DGD Download:Ideal Coordinates CCD File | QB [auth C], RB [auth C], SB [auth C] | DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N | |||
| CLA Download:Ideal Coordinates CCD File | AA [auth A] AB [auth C] BB [auth C] CA [auth A] CB [auth C] | CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M | |||
| PHO Download:Ideal Coordinates CCD File | BA [auth A], WB [auth D] | PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N | |||
| SQD Download:Ideal Coordinates CCD File | EA [auth A] | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N | |||
| LMG Download:Ideal Coordinates CCD File | EC [auth D], IC [auth W], TB [auth C], WA [auth B], YA [auth B] | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N | |||
| PL9 Download:Ideal Coordinates CCD File | BC [auth D] | 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 C53 H80 O2 FKUYMLZIRPABFK-UHFFFAOYSA-N | |||
| LHG Download:Ideal Coordinates CCD File | CC [auth D], DC [auth D], XA [auth B], ZA [auth B] | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N | |||
| HEM Download:Ideal Coordinates CCD File | FC [auth F] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
| BCR Download:Ideal Coordinates CCD File | AC [auth D] DA [auth A] HC [auth K] NB [auth C] OB [auth C] | BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N | |||
| LMU Download:Ideal Coordinates CCD File | UB [auth C] | DODECYL-ALPHA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-YHBSTRCHSA-N | |||
| OEX Download:Ideal Coordinates CCD File | V [auth A] | CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N | |||
| BCT Download:Ideal Coordinates CCD File | XB [auth D] | BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M | |||
| FE2 Download:Ideal Coordinates CCD File | W [auth A] | FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N | |||
| CL Download:Ideal Coordinates CCD File | X [auth A], Y [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | |
| RECONSTRUCTION | RELION | 4.0.1 |
| Funding Organization | Location | Grant Number |
|---|---|---|
| Israel Science Foundation | Israel | 569/17 |