9LP8: Photosystem II protein D1

Extrinsic-protein reconstituted PSII of Thermosynechococcus vulcanus NIES-2134. Determined by X-ray diffraction at 2.0 Å resolution. Released 1 Jul 2026.

Method
X-ray diffraction
Resolution
2.0 Å
Organism
Thermostichus vulcanus NIES-2134
Chains
39
Atoms
54,054
Mol. weight
759.87 kDa
Ligands
OEX, FE2, CLA, PHO
Released
1 Jul 2026

Explore 9LP8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9LP8 contains 299 α-helices and 172 β-strands across 39 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

ElementResiduesLengthSheet
α-helix13-219
α-helix31-5424
β-strand58143
α-helix661
β-strand67143
α-helix681
α-helix71-733
β-strand81-82244
α-helix83-864
α-helix96-983
α-helix102-1076
α-helix110-13627
α-helix143-15513
α-helix156-1605
α-helix161-1655
α-helix168-1703
α-helix172-1732
β-strand174-175244
α-helix176-19015
α-helix192-1943
α-helix196-22126
β-strand223145
β-strand224146
α-helix2251
α-helix233-2364
β-strand243147
β-strand246145
α-helix248-25811
α-helix261-2633
α-helix268-29326
β-strand297-298248
β-strand307149
β-strand313149
α-helix317-33115
Chain b: 27 helices, 24 β-strands
ElementResiduesLengthSheet
β-strand3150
α-helix5-128
α-helix16-4429
α-helix55-573
α-helix63-686
β-strand73151
β-strand79151
α-helix93-11624
β-strand120152
α-helix121-1233
β-strand124153
β-strand131153
α-helix135-15218
α-helix153-1586
β-strand166-168354
β-strand177-179354
α-helix187-1904
α-helix195-21824
α-helix220-2212
β-strand222155
α-helix223-2286
α-helix234-25825
α-helix265-2684
α-helix272-2765
α-helix279-29315
α-helix298-3036
α-helix307-3126
β-strand314156
α-helix315-3173
α-helix319-3213
β-strand323157
α-helix330-3323
β-strand336-342758
β-strand343-347559
β-strand353-354259
β-strand355-356260
α-helix357-3604
β-strand369-371360
β-strand377-380460
β-strand391160
α-helix392-3954
β-strand398-402559
β-strand410-411259
α-helix414-42411
β-strand427156
β-strand429-433558
α-helix447-47428
α-helix476-4783
β-strand482146
α-helix488-4903
β-strand498161
Chain B: 28 helices, 24 β-strands
ElementResiduesLengthSheet
β-strand318
α-helix5-128
α-helix16-4429
α-helix55-573
α-helix63-686
β-strand7319
β-strand7919
α-helix93-11624
β-strand120110
α-helix121-1233
β-strand124111
β-strand131111
α-helix135-15218
α-helix153-1586
β-strand166-168312
β-strand177-179312
α-helix187-1904
α-helix195-21824
α-helix220-2212
β-strand222113
α-helix223-2286
α-helix234-25825
α-helix265-2684
α-helix272-2765
α-helix279-29315
α-helix298-3036
α-helix307-3126
β-strand314114
α-helix315-3173
α-helix319-3213
β-strand323115
α-helix330-3323
β-strand336-342716
β-strand343-347517
β-strand353-354217
β-strand355-356218
α-helix357-3604
β-strand369-371318
β-strand377-380418
β-strand391118
α-helix392-3954
β-strand398-402517
β-strand410-411217
α-helix414-42411
β-strand427114
β-strand429-433516
α-helix447-47428
α-helix476-4783
β-strand48214
α-helix488-4903
β-strand498119
α-helix502-5043
Chain c: 25 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix28-314
α-helix35-428
α-helix46-7328
α-helix81-833
α-helix88-947
β-strand99162
α-helix101-1033
β-strand105162
α-helix109-13022
α-helix131-1355
α-helix154-18128
β-strand185-187363
β-strand195-197363
α-helix206-2138
α-helix223-2264
α-helix230-25324
α-helix258-2636
α-helix268-29225
α-helix299-3024
α-helix306-32318
β-strand332164
β-strand338164
β-strand341-343365
β-strand349-351365
α-helix354-3585
α-helix367-3693
β-strand370-371265
β-strand374-375265
α-helix377-3826
α-helix386-39611
β-strand402-403248
β-strand407166
β-strand408148
α-helix413-4142
β-strand418166
α-helix422-45332
β-strand459167
α-helix461-4633
α-helix465-4684
α-helix470-4712
Chain C: 25 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix28-314
α-helix35-428
α-helix46-7328
α-helix81-833
α-helix88-947
β-strand99120
α-helix101-1033
β-strand105120
α-helix109-13022
α-helix131-1355
α-helix154-18128
β-strand185-187321
β-strand195-197321
α-helix206-2138
α-helix223-2264
α-helix230-25324
α-helix258-2636
α-helix268-29225
α-helix299-3024
α-helix306-32318
β-strand332122
β-strand338122
β-strand341-343323
β-strand349-351323
α-helix353-3586
α-helix367-3693
β-strand370-371223
β-strand374-375223
α-helix377-3826
α-helix386-39611
β-strand402-40326
β-strand407124
β-strand40816
α-helix413-4142
β-strand418124
α-helix422-45332
β-strand459125
α-helix461-4633
α-helix465-4684
α-helix470-4712
Chain d: 24 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix14-229
β-strand24161
α-helix31-5424
β-strand57168
α-helix58-614
β-strand63168
α-helix67-693
β-strand77-78269
α-helix79-824
α-helix83-853
α-helix101-1066
α-helix109-13628
α-helix141-15414
α-helix155-1595
α-helix160-1634
α-helix167-1693
α-helix171-1722
β-strand173-174269
α-helix175-18410
α-helix185-1895
α-helix191-1933
α-helix195-22026
β-strand222170
β-strand223167
α-helix232-2343
β-strand241147
β-strand244170
α-helix246-25712
α-helix264-29027
β-strand294157
α-helix299-3079
α-helix314-33320
α-helix335-3373
α-helix343-3453
Chain D: 23 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix14-229
β-strand24119
α-helix31-5424
β-strand57126
α-helix58-614
β-strand63126
α-helix67-693
β-strand77-78227
α-helix79-824
α-helix83-853
α-helix101-1066
α-helix109-13628
α-helix141-15414
α-helix155-1595
α-helix160-1634
α-helix167-1693
α-helix171-1722
β-strand173-174227
α-helix175-18915
α-helix191-1933
α-helix195-22026
β-strand222128
β-strand223125
α-helix232-2343
β-strand24115
β-strand244128
α-helix246-25712
α-helix264-29027
β-strand294115
α-helix299-3079
α-helix314-33320
α-helix335-3373
α-helix343-3453
Chain e: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix7-93
α-helix10-145
α-helix17-3923
α-helix42-476
α-helix49-513
α-helix72-8110

22 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Photosystem II protein D1A, aprotein360Thermostichus vulcanus NIES-2134P51765 (AlphaFold model)
Photosystem II CP47 reaction center proteinB, bprotein505Thermostichus vulcanus NIES-2134D0VWR1 (AlphaFold model)
Photosystem II 44 kDa reaction center proteinC, cprotein473Thermostichus vulcanus NIES-2134D0VWR7 (AlphaFold model)
Photosystem II D2 proteinD, dprotein342Thermostichus vulcanus NIES-2134D0VWR8 (AlphaFold model)
Cytochrome b559 subunit alphaE, eprotein84Thermostichus vulcanus NIES-2134P12238
Cytochrome b559 subunit betaF, fprotein45Thermostichus vulcanus NIES-2134P12239
Photosystem II reaction center protein HH, hprotein65Thermostichus vulcanus NIES-2134P19052
Photosystem II reaction center protein II, iprotein38Thermostichus vulcanus NIES-2134P12240
Photosystem II reaction center protein JJ, jprotein40Thermostichus vulcanus NIES-2134Q7DGD4
Photosystem II reaction center protein KK, kprotein37Thermostichus vulcanus NIES-2134P19054
Photosystem II reaction center protein LL, lprotein37Thermostichus vulcanus NIES-2134P12241
Photosystem II reaction center protein MM, mprotein36Thermostichus vulcanus NIES-2134P12312

8 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA
>9LP8_1 Photosystem II protein D1 (chains A, a)
MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDI
DGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFL
LGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTF
NFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFG
QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFAALGISTMAFNLNGF
NFNHSVIDAKGNVINTWADIINRANLGMEVMHERNAHNFPLDLASAESAPVAMIAPSING
Sequence of entity 2 (B, b), FASTA
>9LP8_2 Photosystem II CP47 reaction center protein (chains B, b)
GLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMF
VLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLE
LFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQPV
APEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSS
IAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEA
WSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPA
FFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSYA
RKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSG
IDPELSPEQVEWGFYQKVGDVTTRK
Sequence of entity 3 (C, c), FASTA
>9LP8_3 Photosystem II 44 kDa reaction center protein (chains C, c)
MKTLSSQKRYSPVVTLSSNSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLI
VFWAGAMTLFELAHFIPEKPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLI
SSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAM
FFGGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWI
GLICIAGGIWHILTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSE
FYGPTGPEASQAQAMTFLIRDQKLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWD
FRGPWLEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFV
SPRSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD
Sequence of entity 4 (D, d), FASTA
>9LP8_4 Photosystem II D2 protein (chains D, d)
ERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEG
CNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQF
EIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHN
WTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTAN
RFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPE
FETFYTKNLLLNEGIRAWMAPQDQPXENFVFPEEVLPRGNAL
Sequence of entity 5 (E, e), FASTA
>9LP8_5 Cytochrome b559 subunit alpha (chains E, e)
MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQ
RSIPLVTDRFEAKQQVETFLEQLK
Sequence of entity 6 (F, f), FASTA
>9LP8_6 Cytochrome b559 subunit beta (chains F, f)
MTSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR
Sequence of entity 7 (H, h), FASTA
>9LP8_7 Photosystem II reaction center protein H (chains H, h)
ARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVS
WKALG
Sequence of entity 8 (I, i), FASTA
>9LP8_8 Photosystem II reaction center protein I (chains I, i)
METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE
Sequence of entity 9 (J, j), FASTA
>9LP8_9 Photosystem II reaction center protein J (chains J, j)
MMSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL
Sequence of entity 10 (K, k), FASTA
>9LP8_10 Photosystem II reaction center protein K (chains K, k)
KLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR
Sequence of entity 11 (L, l), FASTA
>9LP8_11 Photosystem II reaction center protein L (chains L, l)
MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN
Sequence of entity 12 (M, m), FASTA
>9LP8_12 Photosystem II reaction center protein M (chains M, m)
MEVNQLGLIATALFVLVPSVFLIILYVQTESQQKSS

Ligands and cofactors

IDNameFormulaCopies
OEXCa-MN4-O5 clusterCa Mn4 O52
FE2FE (II) ionFe2
CLAChlorophyll aC55 H72 Mg N4 O570
PHOPheophytin aC55 H74 N4 O54
BCRBeta-caroteneC40 H5620
SQD1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerolC41 H78 O12 S8
LMG1,2-distearoyl-monogalactosyl-diglycerideC45 H86 O1010
PL92,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-he…C53 H80 O24
BCTBicarbonate ionC H O32
CACalcium ionCa7
LMTDodecyl-beta-D-maltosideC24 H46 O1116
HTGheptyl 1-thio-beta-D-glucopyranosideC13 H26 O5 S22
DGDDigalactosyl diacyl glycerol (DGDG)C51 H96 O1510
LHG1,2-dipalmitoyl-phosphatidyl-glyceroleC38 H75 O10 P10
HEMProtoporphyrin IX containing FEC34 H32 Fe N4 O44
RRX(3R)-beta,beta-caroten-3-olC40 H56 O2
MGMagnesium ionMg2

Water and common crystallization additives (CL, UNL, GOL, SO4) are not listed.

Primary citation

Structural basis for impaired oxygen evolution in extrinsic-protein-reconstituted photosystem II. Nakajima, Y., Kato, K., Shen, J.R. et al. ACS Catal (2026).

Other PDB entries of the same protein (UniProt P51765 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 9LP8 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.