9WFZ: Photosystem II reaction center protein I
Cryo-EM structure of PSII PsbA3-S264V from Thermosynechococcus vestitus BP-1 (local refinement). Determined by electron microscopy at 2.08 Å resolution. Released 23 Sept 2026.
- Method
- Electron microscopy
- Resolution
- 2.08 Å
- Organism
- Thermosynechococcus vestitus BP-1
- Chains
- 19
- Atoms
- 17,446
- Mol. weight
- 403.83 kDa
- Ligands
- HEM, DGD, SQD, LMG
- Released
- 23 Sept 2026
Explore 9WFZ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9WFZ contains 119 α-helices and 67 β-strands across 19 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 23 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-21 | 7 | |
| α-helix | 31-54 | 24 | |
| α-helix | 55-57 | 3 | |
| β-strand | 58 | 1 | 3 |
| β-strand | 67 | 1 | 3 |
| α-helix | 71-73 | 3 | |
| β-strand | 81-82 | 2 | 4 |
| α-helix | 83-86 | 4 | |
| α-helix | 96-98 | 3 | |
| α-helix | 102-107 | 6 | |
| α-helix | 110-136 | 27 | |
| α-helix | 143-155 | 13 | |
| α-helix | 156-160 | 5 | |
| α-helix | 161-165 | 5 | |
| α-helix | 168-170 | 3 | |
| α-helix | 172-173 | 2 | |
| β-strand | 174-175 | 2 | 4 |
| α-helix | 176-190 | 15 | |
| α-helix | 192-194 | 3 | |
| α-helix | 196-221 | 26 | |
| β-strand | 223 | 1 | 5 |
| β-strand | 224 | 1 | 6 |
| α-helix | 225 | 1 | |
| α-helix | 233-236 | 4 | |
| β-strand | 243 | 1 | 7 |
| β-strand | 246 | 1 | 5 |
| α-helix | 248-258 | 11 | |
| α-helix | 261-263 | 3 | |
| α-helix | 268-293 | 26 | |
| β-strand | 297-298 | 2 | 8 |
| α-helix | 312-315 | 4 | |
| α-helix | 317-331 | 15 | |
Chain b: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 93-96 | 4 | |
Chain B: 10 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 272-276 | 5 | |
| α-helix | 279-285 | 7 | |
| α-helix | 298-301 | 4 | |
| β-strand | 314 | 1 | 9 |
| α-helix | 315-317 | 3 | |
| α-helix | 319-321 | 3 | |
| β-strand | 323 | 1 | 10 |
| α-helix | 331-334 | 4 | |
| β-strand | 336 | 1 | 11 |
| β-strand | 340-342 | 3 | 12 |
| β-strand | 343-347 | 5 | 13 |
| β-strand | 353-354 | 2 | 13 |
| β-strand | 355-356 | 2 | 14 |
| α-helix | 357-360 | 4 | |
| β-strand | 369-371 | 3 | 14 |
| β-strand | 377-380 | 4 | 14 |
| β-strand | 384 | 1 | 15 |
| β-strand | 391 | 1 | 14 |
| α-helix | 392-395 | 4 | |
| β-strand | 398-402 | 5 | 13 |
| β-strand | 409-411 | 3 | 13 |
| α-helix | 416-424 | 9 | |
| β-strand | 427 | 1 | 9 |
| β-strand | 429-430 | 2 | 12 |
| β-strand | 433 | 1 | 11 |
| β-strand | 482 | 1 | 6 |
| α-helix | 488-491 | 4 | |
| β-strand | 498 | 1 | 16 |
Chain C: 19 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-31 | 4 | |
| α-helix | 35-42 | 8 | |
| α-helix | 46-73 | 28 | |
| α-helix | 81-83 | 3 | |
| α-helix | 89-92 | 4 | |
| α-helix | 109-134 | 26 | |
| α-helix | 223-226 | 4 | |
| α-helix | 268-292 | 25 | |
| α-helix | 299-302 | 4 | |
| α-helix | 306-323 | 18 | |
| α-helix | 328-330 | 3 | |
| β-strand | 332 | 1 | 17 |
| β-strand | 338 | 1 | 17 |
| β-strand | 341-343 | 3 | 18 |
| β-strand | 349-351 | 3 | 18 |
| α-helix | 353-358 | 6 | |
| α-helix | 367-369 | 3 | |
| β-strand | 370-371 | 2 | 18 |
| β-strand | 374-375 | 2 | 18 |
| α-helix | 377-382 | 6 | |
| α-helix | 386-396 | 11 | |
| β-strand | 402-403 | 2 | 8 |
| β-strand | 408 | 1 | 8 |
| α-helix | 422-453 | 32 | |
| β-strand | 459 | 1 | 19 |
| α-helix | 461-463 | 3 | |
| α-helix | 466-468 | 3 | |
| α-helix | 470-471 | 2 | |
Chain D: 23 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24 | 1 | 16 |
| α-helix | 31-54 | 24 | |
| β-strand | 57 | 1 | 20 |
| β-strand | 63 | 1 | 20 |
| α-helix | 67-69 | 3 | |
| β-strand | 77-78 | 2 | 21 |
| α-helix | 79-82 | 4 | |
| α-helix | 83-85 | 3 | |
| α-helix | 101-106 | 6 | |
| α-helix | 109-136 | 28 | |
| α-helix | 141-153 | 13 | |
| α-helix | 154-159 | 6 | |
| α-helix | 160-163 | 4 | |
| α-helix | 167-169 | 3 | |
| α-helix | 171-172 | 2 | |
| β-strand | 173-174 | 2 | 21 |
| α-helix | 175-184 | 10 | |
| α-helix | 185-189 | 5 | |
| α-helix | 191-193 | 3 | |
| α-helix | 195-220 | 26 | |
| β-strand | 222 | 1 | 22 |
| β-strand | 223 | 1 | 19 |
| α-helix | 231-234 | 4 | |
| β-strand | 241 | 1 | 7 |
| β-strand | 244 | 1 | 22 |
| α-helix | 246-257 | 12 | |
| α-helix | 264-289 | 26 | |
| β-strand | 294 | 1 | 10 |
| α-helix | 299-307 | 9 | |
| α-helix | 314-323 | 10 | |
| α-helix | 330-333 | 4 | |
| α-helix | 335-337 | 3 | |
| α-helix | 343-345 | 3 | |
Chain E: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-9 | 2 | |
| α-helix | 10-14 | 5 | |
| α-helix | 23-37 | 15 | |
| α-helix | 44-47 | 4 | |
| α-helix | 72-81 | 10 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-40 | 23 | |
Chain I: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-22 | 21 | |
| α-helix | 27-29 | 3 | |
11 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Photosystem II reaction center protein I | I | protein | 38 | Thermosynechococcus vestitus BP-1 | Q8DJZ6 (AlphaFold model) |
| Photosystem II reaction center protein K | K | protein | 46 | Thermosynechococcus vestitus BP-1 | Q9F1K9 (AlphaFold model) |
| Photosystem II reaction center protein T | T | protein | 32 | Thermosynechococcus vestitus BP-1 | Q8DIQ0 (AlphaFold model) |
| Photosystem II extrinsic protein V | V | protein | 163 | Thermosynechococcus vestitus BP-1 | P0A386 (AlphaFold model) |
| Photosystem II reaction center protein Psb30 | Y | protein | 46 | Thermosynechococcus vestitus BP-1 | Q8DJI1 |
| Photosystem II protein D1 3 | A | protein | 360 | Thermosynechococcus vestitus BP-1 | Q8DIV4 |
| Photosystem II CP47 reaction center protein | B, b | protein | 510 | Thermosynechococcus vestitus BP-1 | Q8DIQ1 |
| Photosystem II CP43 reaction center protein | C | protein | 461 | Thermosynechococcus vestitus BP-1 | Q8DIF8 |
| Photosystem II D2 protein | D | protein | 352 | Thermosynechococcus vestitus BP-1 | Q8CM25 |
| Cytochrome b559 subunit alpha | E | protein | 84 | Thermosynechococcus vestitus BP-1 | Q8DIP0 |
| Cytochrome b559 subunit beta | F | protein | 45 | Thermosynechococcus vestitus BP-1 | Q8DIN9 |
| Photosystem II reaction center protein J | J | protein | 40 | Thermosynechococcus vestitus BP-1 | P59087 |
6 more molecules are not listed.
Sequence of entity 1 (I), FASTA
>9WFZ_1 Photosystem II reaction center protein I (chains I)
METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE
Sequence of entity 2 (K), FASTA
>9WFZ_2 Photosystem II reaction center protein K (chains K)
MIDALVLVAKLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR
Sequence of entity 3 (T), FASTA
>9WFZ_3 Photosystem II reaction center protein T (chains T)
METITYVFIFACIIALFFFAIFFREPPRITKK
Sequence of entity 4 (V), FASTA
>9WFZ_4 Photosystem II extrinsic protein V (chains V)
MLKKCVWLAVALCLCLWQFTMGTALAAELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQ
YACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPS
LRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWGGGKVYY
Sequence of entity 5 (Y), FASTA
>9WFZ_5 Photosystem II reaction center protein Psb30 (chains Y)
MGIFNGIIEFLSNINFEVIAQLTMIAMIGIAGPMIIFLLAVRRGNL
Sequence of entity 6 (A), FASTA
>9WFZ_6 Photosystem II protein D1 3 (chains A)
MTTVLQRREQLNLWEQFCSWVTSTNNRLYVGWFGVLMIPTLLAATICFVIAFIAAPPVDI
DGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFL
IGVFCYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTF
NFMLVFQAEHNILMHPFHQLGVAGVFGGALFSAMHGSLVTSSLIRETTETESANYGYKFG
QEEETYNIVAAHGYFGRLIFQYAVFNNSRALHFFLAAWPVIGIWFTALGISTMAFNLNGF
NFNHSVVDAQGNVINTWADIINRANLGMEVMHERNAHNFPLDLASAESAPVAMIAPSING
Sequence of entity 7 (B, b), FASTA
>9WFZ_7 Photosystem II CP47 reaction center protein (chains B, b)
MGLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGM
FVLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDL
ELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQP
VAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSS
SIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEE
AWSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMP
AFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSY
ARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFS
GIDPELSPEQVEWGFYQKVGDVTTRRKEAV
Sequence of entity 8 (C), FASTA
>9WFZ_8 Photosystem II CP43 reaction center protein (chains C)
MVTLSSNSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFEL
AHFIPEKPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYH
AIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPG
GGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHI
LTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQA
QAMTFLIRDQKLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGP
NGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFV
LAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD
Sequence of entity 9 (D), FASTA
>9WFZ_9 Photosystem II D2 protein (chains D)
MTIAIGRAPAERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYT
HGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAF
GLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFR
FLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQA
EETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFIS
QEIRAAEDPEFETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL
Sequence of entity 10 (E), FASTA
>9WFZ_10 Cytochrome b559 subunit alpha (chains E)
MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQ
RSIPLVTDRFEAKQQVETFLEQLK
Sequence of entity 11 (F), FASTA
>9WFZ_11 Cytochrome b559 subunit beta (chains F)
MTSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR
Sequence of entity 12 (J), FASTA
>9WFZ_12 Photosystem II reaction center protein J (chains J)
MMSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 1 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 4 |
| SQD | 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol | C41 H78 O12 S | 2 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 3 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 5 |
| BCT | Bicarbonate ion | C H O3 | 1 |
| PL9 | 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-he… | C53 H80 O2 | 2 |
| PHO | Pheophytin a | C55 H74 N4 O5 | 2 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 22 |
| FE2 | FE (II) ion | Fe | 1 |
| OEX | Ca-MN4-O5 cluster | Ca Mn4 O5 | 1 |
| HEC | Heme C | C34 H36 Fe N4 O4 | 1 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 3 |
| BCR | Beta-carotene | C40 H56 | 8 |
Water and common crystallization additives (CL, UNL) are not listed.
Primary citation
Structural and functional analysis of a photosystem II mutant PsbA3-S264V. Fan, S., Nakajima, Y., Kato, K. et al. Biochim Biophys Acta Bioenerg (2026) 1868:149607-149607. DOI 10.1016/j.bbabio.2026.149607 · PubMed
Other PDB entries of the same protein (UniProt Q8DJZ6 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9EVX 1.71 Å, cryoEM structure of Photosystem II averaged across S2-S3 states at 1.71 Angstrom…
- 9M5A 1.88 Å, cryo-EM structure of PSII D1-V185T from Thermosynechococcus vestitus BP-1
- 7RF1 1.89 Å, RT XFEL structure of Photosystem II averaged across all S-states at 1.89 Angstrom…
- 7YQ2 1.9 Å, Crystal structure of photosystem II expressing psbA2 gene only
- 7YQ7 1.9 Å, Crystal structure of photosystem II expressing psbA3 gene only
- 9Z35 1.93 Å, RT XFEL structure of two-flash state of Photosystem II (2F, S3 rich) at 1.93 Angstrom…
- 9Z6A 1.93 Å, RT XFEL structure of the two-flash state of Photosystem II (2F, S3 rich) at 1.93…
- 9W5B 1.96 Å, cryo-EM structure of PSII D1-S264V from Thermosynechococcus vestitus BP-1
- 9Z33 1.97 Å, RT XFEL structure of dark-stable state of Photosystem II (0F, S1 rich) at 1.97 Angstrom…
- 9Z68 1.97 Å, RT XFEL structure of the dark-stable state of Photosystem II (0F, S1 rich) at 1.97…
- 9Z34 1.98 Å, RT XFEL structure of one-flash state of Photosystem II (1F, S2 rich) at 1.98 Angstrom…
- 9Z69 1.98 Å, RT XFEL structure of the one-flash state of Photosystem II (1F, S2 rich) at 1.98…
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