STRUCTURE OF UNSTACKED C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM
Klaiman, D., Fadeeva, M., Nelson, N.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 | A, Z [auth a] | 334 | Lathyrus oleraceus | Mutation(s): 0  EC: 1.10.3.9 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06585 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II CP47 reaction center protein | AA [auth b], B | 503 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D5MAL6 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II CP43 reaction center protein | BA [auth c], C | 450 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06004 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II D2 protein | CA [auth d], D | 352 | Lathyrus oleraceus | Mutation(s): 0  EC: 1.10.3.9 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06006 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b559 subunit alpha | DA [auth e], E | 75 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13554 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b559 subunit beta | EA [auth f], F | 30 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P62096 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chlorophyll a-b binding protein 8, chloroplastic | FA [auth g], G, MA [auth n], N | 216 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P27490 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein H | GA [auth h], H | 60 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9XQR3 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein I | HA [auth i], I | 34 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D5MAJ9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 10 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein J | IA [auth j], J | 35 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13555 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 11 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein K | JA [auth k], K | 37 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D5MAJ8 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 12 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein L | KA [auth l], L | 36 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P60147 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 13 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein M | LA [auth m], M | 33 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P69529 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 14 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Oxygen-evolving enhancer protein 1, chloroplastic | NA [auth o], O | 248 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P14226 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 15 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Oxygen-evolving enhancer protein 2, chloroplastic | OA [auth p], P | 186 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P16059 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 16 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Oxygen-evolving enhancer protein 3 | PA [auth q], Q | 148 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7Y1T5 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 17 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chlorophyll a-b binding protein, chloroplastic | QA [auth r], R | 224 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for A0A2D0TCJ0 (Pisum sativum) Explore A0A2D0TCJ0  Go to UniProtKB:  A0A2D0TCJ0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2D0TCJ0 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 18 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chlorophyll a-b binding protein, chloroplastic | RA [auth s], S | 218 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for A0A9D5GXR9 (Pisum sativum) Explore A0A9D5GXR9  Go to UniProtKB:  A0A9D5GXR9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A9D5GXR9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 19 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein T | SA [auth t], T | 31 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8HS25 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 20 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein W | TA [auth w], U [auth W] | 54 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for A0A2D0TCJ2 (Pisum sativum) Explore A0A2D0TCJ2  Go to UniProtKB:  A0A2D0TCJ2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2D0TCJ2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 21 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ultraviolet-B-repressible protein | UA [auth x], V [auth X] | 39 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8VYY1 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 22 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chlorophyll a-b binding protein AB80, chloroplastic | VA [auth y], W [auth Y] | 219 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07371 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 23 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II reaction center protein Z | WA [auth z], X [auth Z] | 61 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q32902 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 24 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Photosystem II 5 kDa protein, chloroplastic | XA [auth u], Y [auth U] | 28 | Lathyrus oleraceus | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for A0A9D4VSA9 (Pisum sativum) Explore A0A9D4VSA9  Go to UniProtKB:  A0A9D4VSA9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A9D4VSA9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
| Ligands 17 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DGD Download:Ideal Coordinates CCD File | FD [auth C] GD [auth C] HD [auth C] MH [auth a] OB [auth A] | DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N | |||
| CHL Download:Ideal Coordinates CCD File | AE [auth G] AF [auth N] AH [auth Y] AM [auth r] BE [auth G] | CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M | |||
| CLA Download:Ideal Coordinates CCD File | AC [auth B] AD [auth C] AJ [auth c] BC [auth B] BD [auth C] | CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M | |||
| PHO Download:Ideal Coordinates CCD File | EB [auth A], MD [auth D], TH [auth a], WJ [auth d] | PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N | |||
| SQD Download:Ideal Coordinates CCD File | HB [auth A] IC [auth B] LB [auth A] OE [auth L] QE [auth L] | 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 | BL [auth k] DK [auth d] EN [auth w] IB [auth A] ID [auth C] | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N | |||
| PL9 Download:Ideal Coordinates CCD File | BK [auth d], JB [auth A], QD [auth D], XH [auth a] | 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 | AG [auth S] AI [auth a] CK [auth d] CL [auth l] CN [auth s] | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N | |||
| HEM Download:Ideal Coordinates CCD File | EK [auth f], TD [auth E] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
| XAT Download:Ideal Coordinates CCD File | JH [auth Y], JM [auth r], WN [auth y], YF [auth R] | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O4 SZCBXWMUOPQSOX-WVJDLNGLSA-N | |||
| NEX Download:Ideal Coordinates CCD File | BN [auth s] GN [auth y] IF [auth N] KE [auth G] KH [auth Y] | (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL C40 H56 O4 PGYAYSRVSAJXTE-OQASCVKESA-N | |||
| LUT Download:Ideal Coordinates CCD File | AN [auth s] GF [auth N] HF [auth N] HH [auth Y] IE [auth G] | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O2 KBPHJBAIARWVSC-NSIPBSJQSA-N | |||
| BCR Download:Ideal Coordinates CCD File | AK [auth d] AL [auth k] CD [auth C] DD [auth C] DN [auth t] | BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N | |||
| OEX Download:Ideal Coordinates CCD File | NH [auth a], YA [auth A] | CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N | |||
| BCT Download:Ideal Coordinates CCD File | MB [auth A], XJ [auth d] | BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M | |||
| FE2 Download:Ideal Coordinates CCD File | OH [auth a], ZA [auth A] | FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N | |||
| CL Download:Ideal Coordinates CCD File | AB [auth A], BB [auth A], PH [auth a], QH [auth a] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | RELION | 4.0.0 |
| Funding Organization | Location | Grant Number |
|---|---|---|
| Israel Science Foundation | Israel | 199/21 |