9W5B: Photosystem II protein D1 3
cryo-EM structure of PSII D1-S264V from Thermosynechococcus vestitus BP-1. Determined by electron microscopy at 1.96 Å resolution. Released 23 Sept 2026.
- Method
- Electron microscopy
- Resolution
- 1.96 Å
- Organism
- Thermosynechococcus vestitus BP-1
- Chains
- 38
- Atoms
- 47,744
- Mol. weight
- 735.63 kDa
- Ligands
- OEX, FE2, CLA, BCR
- Released
- 23 Sept 2026
Explore 9W5B in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9W5B contains 294 α-helices and 176 β-strands across 38 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.
Chains a and A: 23 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-21 | 9 | |
| α-helix | 31-54 | 24 | |
| α-helix | 55-57 | 3 | |
| β-strand | 58 | 1 | 46 |
| β-strand | 67 | 1 | 46 |
| α-helix | 71-73 | 3 | |
| β-strand | 81-82 | 2 | 47 |
| 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 | 47 |
| α-helix | 176-190 | 15 | |
| α-helix | 192-194 | 3 | |
| α-helix | 196-221 | 26 | |
| β-strand | 223 | 1 | 48 |
| β-strand | 224 | 1 | 49 |
| α-helix | 233-236 | 4 | |
| β-strand | 243 | 1 | 50 |
| β-strand | 246 | 1 | 48 |
| α-helix | 248-258 | 11 | |
| α-helix | 261-263 | 3 | |
| α-helix | 268-293 | 26 | |
| β-strand | 297-298 | 2 | 51 |
| β-strand | 307 | 1 | 52 |
| α-helix | 312 | 1 | |
| β-strand | 313 | 1 | 52 |
| α-helix | 314-315 | 2 | |
| α-helix | 317-331 | 15 | |
Chains b and B: 27 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 53 |
| α-helix | 5-12 | 8 | |
| α-helix | 16-44 | 29 | |
| α-helix | 55-57 | 3 | |
| α-helix | 63-68 | 6 | |
| β-strand | 73 | 1 | 54 |
| β-strand | 79 | 1 | 54 |
| α-helix | 93-116 | 24 | |
| β-strand | 120 | 1 | 55 |
| α-helix | 121-123 | 3 | |
| β-strand | 124 | 1 | 56 |
| β-strand | 131 | 1 | 56 |
| α-helix | 135-152 | 18 | |
| α-helix | 153-158 | 6 | |
| β-strand | 166-168 | 3 | 57 |
| β-strand | 177-179 | 3 | 57 |
| α-helix | 187-190 | 4 | |
| α-helix | 195-218 | 24 | |
| α-helix | 220-221 | 2 | |
| β-strand | 222 | 1 | 58 |
| α-helix | 223-228 | 6 | |
| α-helix | 234-258 | 25 | |
| α-helix | 265-268 | 4 | |
| α-helix | 272-276 | 5 | |
| α-helix | 279-293 | 15 | |
| α-helix | 298-303 | 6 | |
| α-helix | 307-312 | 6 | |
| β-strand | 314 | 1 | 59 |
| α-helix | 315-317 | 3 | |
| α-helix | 319-321 | 3 | |
| β-strand | 323 | 1 | 60 |
| α-helix | 331-334 | 4 | |
| β-strand | 336-340 | 5 | 61 |
| β-strand | 343-347 | 5 | 62 |
| β-strand | 353-354 | 2 | 62 |
| β-strand | 355-356 | 2 | 63 |
| α-helix | 357-360 | 4 | |
| β-strand | 369-371 | 3 | 63 |
| β-strand | 377-380 | 4 | 63 |
| β-strand | 384 | 1 | 64 |
| α-helix | 392-395 | 4 | |
| β-strand | 398-402 | 5 | 62 |
| β-strand | 410-411 | 2 | 62 |
| α-helix | 414-424 | 11 | |
| β-strand | 427 | 1 | 59 |
| β-strand | 430-433 | 4 | 61 |
| α-helix | 447-474 | 28 | |
| α-helix | 476-478 | 3 | |
| β-strand | 482 | 1 | 49 |
| α-helix | 488-490 | 3 | |
| β-strand | 498 | 1 | 65 |
Chains c and C: 22 helices, 13 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 | 89-94 | 6 | |
| β-strand | 99 | 1 | 66 |
| α-helix | 101-103 | 3 | |
| β-strand | 105 | 1 | 66 |
| α-helix | 109-130 | 22 | |
| α-helix | 131-135 | 5 | |
| α-helix | 154-180 | 27 | |
| β-strand | 185-187 | 3 | 67 |
| β-strand | 195-197 | 3 | 67 |
| α-helix | 206-212 | 7 | |
| α-helix | 223-226 | 4 | |
| α-helix | 230-253 | 24 | |
| α-helix | 258-263 | 6 | |
| α-helix | 268-292 | 25 | |
| α-helix | 299-302 | 4 | |
| α-helix | 306-323 | 18 | |
| β-strand | 332 | 1 | 68 |
| β-strand | 338 | 1 | 68 |
| β-strand | 341-343 | 3 | 69 |
| β-strand | 349-351 | 3 | 69 |
| α-helix | 354-358 | 5 | |
| α-helix | 367-369 | 3 | |
| β-strand | 370-371 | 2 | 69 |
| β-strand | 374-375 | 2 | 69 |
| α-helix | 377-382 | 6 | |
| α-helix | 386-396 | 11 | |
| β-strand | 402-403 | 2 | 51 |
| β-strand | 408 | 1 | 51 |
| α-helix | 422-453 | 32 | |
| β-strand | 459 | 1 | 70 |
| α-helix | 466-468 | 3 | |
Chains d and D: 22 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-22 | 9 | |
| β-strand | 24 | 1 | 65 |
| α-helix | 31-54 | 24 | |
| β-strand | 57 | 1 | 71 |
| β-strand | 63 | 1 | 71 |
| α-helix | 67-69 | 3 | |
| β-strand | 77-78 | 2 | 72 |
| 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 | 72 |
| α-helix | 175-184 | 10 | |
| α-helix | 185-189 | 5 | |
| α-helix | 191-193 | 3 | |
| α-helix | 195-220 | 26 | |
| β-strand | 222 | 1 | 73 |
| β-strand | 223 | 1 | 70 |
| β-strand | 241 | 1 | 50 |
| β-strand | 244 | 1 | 73 |
| α-helix | 246-257 | 12 | |
| α-helix | 264-289 | 26 | |
| β-strand | 294 | 1 | 60 |
| α-helix | 299-307 | 9 | |
| α-helix | 314-333 | 20 | |
| α-helix | 335-337 | 3 | |
| α-helix | 343-345 | 3 | |
Chains e and E: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-9 | 2 | |
| α-helix | 10-14 | 5 | |
| α-helix | 17-39 | 23 | |
| α-helix | 42-47 | 6 | |
| α-helix | 49-51 | 3 | |
| α-helix | 72-81 | 10 | |
Chains f and F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-40 | 23 | |
Chains h and H: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 55 |
| α-helix | 6-11 | 6 | |
| α-helix | 12-15 | 4 | |
| β-strand | 22 | 1 | 58 |
| α-helix | 28-49 | 22 | |
| β-strand | 55 | 1 | 74 |
| β-strand | 58 | 1 | 74 |
Chains i and I: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-23 | 22 | |
| 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 protein D1 3 | A, a | protein | 360 | Thermosynechococcus vestitus BP-1 | Q8DIV4 (AlphaFold model) |
| Photosystem II CP47 reaction center protein | B, b | protein | 510 | Thermosynechococcus vestitus BP-1 | Q8DIQ1 (AlphaFold model) |
| Photosystem II CP43 reaction center protein | C, c | protein | 461 | Thermosynechococcus vestitus BP-1 | Q8DIF8 (AlphaFold model) |
| Photosystem II D2 protein | D, d | protein | 352 | Thermosynechococcus vestitus BP-1 | Q8CM25 (AlphaFold model) |
| Cytochrome b559 subunit alpha | E, e | protein | 84 | Thermosynechococcus vestitus BP-1 | Q8DIP0 |
| Cytochrome b559 subunit beta | F, f | protein | 45 | Thermosynechococcus vestitus BP-1 | Q8DIN9 |
| Photosystem II reaction center protein H | H, h | protein | 66 | Thermosynechococcus vestitus BP-1 | Q8DJ43 |
| Photosystem II reaction center protein I | I, i | protein | 38 | Thermosynechococcus vestitus BP-1 | Q8DJZ6 |
| Photosystem II reaction center protein J | J, j | protein | 40 | Thermosynechococcus vestitus BP-1 | P59087 |
| Photosystem II reaction center protein K | K, k | protein | 46 | Thermosynechococcus vestitus BP-1 | Q9F1K9 |
| Photosystem II reaction center protein L | L, l | protein | 37 | Thermosynechococcus vestitus BP-1 | Q8DIN8 |
| Photosystem II reaction center protein M | M, m | protein | 36 | Thermosynechococcus vestitus BP-1 | Q8DHA7 |
7 more molecules are not listed.
Sequence of entity 1 (A, a), FASTA
>9W5B_1 Photosystem II protein D1 3 (chains A, a)
MTTVLQRREQLNLWEQFCSWVTSTNNRLYVGWFGVLMIPTLLAATICFVIAFIAAPPVDI
DGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFL
IGVFCYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTF
NFMLVFQAEHNILMHPFHQLGVAGVFGGALFSAMHGSLVTSSLIRETTETESANYGYKFG
QEEETYNIVAAHGYFGRLIFQYAVFNNSRALHFFLAAWPVIGIWFTALGISTMAFNLNGF
NFNHSVVDAQGNVINTWADIINRANLGMEVMHERNAHNFPLDLASAESAPVAMIAPSING
Sequence of entity 2 (B, b), FASTA
>9W5B_2 Photosystem II CP47 reaction center protein (chains B, b)
MGLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGM
FVLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDL
ELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQP
VAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSS
SIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEE
AWSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMP
AFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSY
ARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFS
GIDPELSPEQVEWGFYQKVGDVTTRRKEAV
Sequence of entity 3 (C, c), FASTA
>9W5B_3 Photosystem II CP43 reaction center protein (chains C, c)
MVTLSSNSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFEL
AHFIPEKPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYH
AIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPG
GGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHI
LTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQA
QAMTFLIRDQKLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGP
NGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFV
LAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD
Sequence of entity 4 (D, d), FASTA
>9W5B_4 Photosystem II D2 protein (chains D, d)
MTIAIGRAPAERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYT
HGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAF
GLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFR
FLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQA
EETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFIS
QEIRAAEDPEFETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL
Sequence of entity 5 (E, e), FASTA
>9W5B_5 Cytochrome b559 subunit alpha (chains E, e)
MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQ
RSIPLVTDRFEAKQQVETFLEQLK
Sequence of entity 6 (F, f), FASTA
>9W5B_6 Cytochrome b559 subunit beta (chains F, f)
MTSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR
Sequence of entity 7 (H, h), FASTA
>9W5B_7 Photosystem II reaction center protein H (chains H, h)
MARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNV
SWKALG
Sequence of entity 8 (I, i), FASTA
>9W5B_8 Photosystem II reaction center protein I (chains I, i)
METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE
Sequence of entity 9 (J, j), FASTA
>9W5B_9 Photosystem II reaction center protein J (chains J, j)
MMSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL
Sequence of entity 10 (K, k), FASTA
>9W5B_10 Photosystem II reaction center protein K (chains K, k)
MIDALVLVAKLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR
Sequence of entity 11 (L, l), FASTA
>9W5B_11 Photosystem II reaction center protein L (chains L, l)
MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN
Sequence of entity 12 (M, m), FASTA
>9W5B_12 Photosystem II reaction center protein M (chains M, m)
MEVNQLGLIATALFVLVPSVFLIILYVQTESQQKSS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| OEX | Ca-MN4-O5 cluster | Ca Mn4 O5 | 2 |
| FE2 | FE (II) ion | Fe | 2 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 70 |
| BCR | Beta-carotene | C40 H56 | 20 |
| SQD | 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol | C41 H78 O12 S | 4 |
| 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 | 4 |
| BCT | Bicarbonate ion | C H O3 | 2 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 10 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 6 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 6 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 8 |
| PHO | Pheophytin a | C55 H74 N4 O5 | 4 |
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 2 |
| CA | Calcium ion | Ca | 2 |
| HEC | Heme C | C34 H36 Fe N4 O4 | 2 |
| RRX | (3R)-beta,beta-caroten-3-ol | C40 H56 O | 2 |
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 Q8DIV4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9M5A 1.88 Å, cryo-EM structure of PSII D1-V185T from Thermosynechococcus vestitus BP-1
- 7YQ7 1.9 Å, Crystal structure of photosystem II expressing psbA3 gene only
- 5OJR 1.96 Å, YCF48 bound to D1 peptide
- 9W7D 2.05 Å, cryo-EM structure of PSII PsbA3-S264V in complex with DCMU from Thermosynechococcus…
- 9WFZ 2.08 Å, Cryo-EM structure of PSII PsbA3-S264V from Thermosynechococcus vestitus BP-1 (local…
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