7YQ2: Photosystem II expressing psbA2 gene only

Crystal structure of photosystem II expressing psbA2 gene only. Determined by X-ray diffraction at 1.9 Å resolution. Released 30 Nov 2022.

Method
X-ray diffraction
Resolution
1.9 Å
Organism
Thermosynechococcus vestitus BP-1
Chains
39
Atoms
55,630
Mol. weight
793.82 kDa
Ligands
OEX, FE2, CLA, PHO
Released
30 Nov 2022

Explore 7YQ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YQ2 contains 303 α-helices and 174 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.

Chain a: 23 helices, 11 β-strands

ElementResiduesLengthSheet
α-helix10-2112
α-helix31-5424
β-strand58144
α-helix661
β-strand67144
α-helix681
α-helix71-733
β-strand81-82245
α-helix83-864
α-helix96-983
α-helix102-1076
α-helix110-13728
α-helix143-15513
α-helix156-1605
α-helix161-1655
α-helix168-1703
α-helix172-1732
β-strand174-175245
α-helix176-19015
α-helix192-1943
α-helix196-22126
β-strand223146
β-strand224147
α-helix2251
α-helix233-2364
β-strand243148
β-strand246146
α-helix248-25811
α-helix261-2633
α-helix268-29326
β-strand297-298249
β-strand307150
β-strand313150
α-helix317-33115
Chain A: 24 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix13-219
α-helix31-5424
α-helix55-573
β-strand5811
α-helix661
β-strand6711
α-helix681
α-helix71-733
β-strand81-8222
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-strand174-17522
α-helix176-19015
α-helix192-1943
α-helix196-22126
β-strand22313
β-strand22414
α-helix2251
α-helix233-2364
β-strand24315
β-strand24613
α-helix248-25811
α-helix261-2633
α-helix268-29326
β-strand297-29826
β-strand30717
β-strand31317
α-helix317-33115
Chain b: 27 helices, 24 β-strands
ElementResiduesLengthSheet
β-strand3151
α-helix5-128
α-helix16-4429
α-helix55-573
α-helix63-686
β-strand73152
β-strand79152
α-helix93-11624
β-strand120153
α-helix121-1233
β-strand124154
β-strand131154
α-helix135-15218
α-helix153-1586
β-strand166-168355
β-strand177-179355
α-helix187-1904
α-helix195-21824
α-helix220-2212
β-strand222156
α-helix223-2286
α-helix234-25825
α-helix265-2684
α-helix272-2765
α-helix279-29315
α-helix298-3036
α-helix307-3126
β-strand314157
α-helix315-3173
β-strand323158
α-helix330-3323
β-strand336-342759
β-strand343-347560
β-strand353-354260
β-strand355-356261
α-helix357-3604
β-strand369-371361
β-strand377-380461
β-strand391161
α-helix392-3954
β-strand398-402560
β-strand410-411260
α-helix414-42411
β-strand427157
β-strand429-433559
α-helix447-47428
α-helix476-4783
β-strand482147
α-helix488-4914
β-strand498162
α-helix502-5043
Chain B: 27 helices, 26 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
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-strand496119
β-strand498120
α-helix502-5043
β-strand505119
Chains c and C: 25 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix28-314
α-helix35-428
α-helix46-7429
α-helix81-833
α-helix88-947
β-strand99163
α-helix101-1033
β-strand105163
α-helix109-13022
α-helix131-1355
α-helix154-18128
β-strand185-187364
β-strand195-197364
α-helix206-2138
α-helix223-2264
α-helix230-25324
α-helix258-2636
α-helix268-29225
α-helix299-3024
α-helix306-32318
β-strand332165
β-strand338165
β-strand341-343366
β-strand349-351366
α-helix353-3586
α-helix367-3693
β-strand370-371266
β-strand374-375266
α-helix377-3826
α-helix386-39611
β-strand402-403249
β-strand407167
β-strand408149
α-helix413-4142
β-strand418167
α-helix422-45332
β-strand459168
α-helix461-4633
α-helix465-4684
α-helix470-4712
Chain d: 22 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix14-229
β-strand24162
α-helix31-5424
β-strand57169
α-helix58-614
β-strand63169
α-helix67-693
β-strand77-78270
α-helix79-824
α-helix83-853
α-helix101-1077
α-helix109-13628
α-helix141-15313
α-helix154-1596
α-helix160-1634
α-helix167-1693
α-helix171-1722
β-strand173-174270
α-helix175-18915
α-helix191-1933
α-helix195-21925
β-strand222171
β-strand223168
β-strand241148
β-strand244171
α-helix246-25712
α-helix264-28926
β-strand294158
α-helix299-3079
α-helix314-33320
α-helix335-3373
α-helix343-3453
Chain D: 22 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix14-229
β-strand24120
α-helix31-5424
β-strand57127
α-helix58-614
β-strand63127
α-helix67-693
β-strand77-78228
α-helix79-824
α-helix83-853
α-helix101-1077
α-helix109-13628
α-helix141-15414
α-helix155-1595
α-helix160-1634
α-helix167-1693
α-helix171-1722
β-strand173-174228
α-helix175-18915
α-helix191-1933
α-helix195-22026
β-strand222129
β-strand223126
β-strand24115
β-strand244129
α-helix246-25712
α-helix264-28926
β-strand294115
α-helix299-3079
α-helix314-33320
α-helix335-3373
α-helix343-3453
Chain e: 7 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix7-93
α-helix10-145
α-helix17-3923
α-helix42-476
α-helix49-513
α-helix52-543
α-helix72-8110

20 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 D1 2A, aprotein360Thermosynechococcus vestitus BP-1P0A446 (AlphaFold model)
Photosystem II CP47 reaction center proteinB, bprotein510Thermosynechococcus vestitus BP-1Q8DIQ1 (AlphaFold model)
Photosystem II CP43 reaction center proteinC, cprotein461Thermosynechococcus vestitus BP-1Q8DIF8 (AlphaFold model)
Photosystem II D2 proteinD, dprotein352Thermosynechococcus vestitus BP-1Q8CM25 (AlphaFold model)
Cytochrome b559 subunit alphaE, eprotein84Thermosynechococcus vestitus BP-1Q8DIP0
Cytochrome b559 subunit betaF, fprotein45Thermosynechococcus vestitus BP-1Q8DIN9
Photosystem II reaction center protein HH, hprotein66Thermosynechococcus vestitus BP-1Q8DJ43
Photosystem II reaction center protein II, iprotein38Thermosynechococcus vestitus BP-1Q8DJZ6
Photosystem II reaction center protein JJ, jprotein40Thermosynechococcus vestitus BP-1P59087
Photosystem II reaction center protein KK, kprotein46Thermosynechococcus vestitus BP-1Q9F1K9
Photosystem II reaction center protein LL, lprotein37Thermosynechococcus vestitus BP-1Q8DIN8
Photosystem II reaction center protein MM, mprotein36Thermosynechococcus vestitus BP-1Q8DHA7

8 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA
>7YQ2_1 Photosystem II protein D1 2 (chains A, a)
MTTVLQRRQTANLWERFCDWITSTENRLYIGWFGVIMIPTLLAATICFVIAFIAAPPVDI
DGIREPVSGSLLYGNNIITAAVVPSSNAIGLHLYPIWDAASLDEWLYNGGPYQLIIFHFL
IGIFCYMGREWELSYRLGMRPWIPVAFSAPVAAATAVLLIYPIGQGSFSDGLMLGISGTF
NFMIVFQAEHNILMHPFHMLGVAGVFGGALFAAMHGSLVTSSLIRETTETESTNYGYKFG
QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFAALGISTMAFNLNGF
NFNHSVVDAQGNVINTWADIINRANIGIEVMHERNAHNFPLDLASGELAPVAMIAPSIEA
Sequence of entity 2 (B, b), FASTA
>7YQ2_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
>7YQ2_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
>7YQ2_4 Photosystem II D2 protein (chains D, d)
MTIAIGRAPAERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYT
HGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAF
GLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFR
FLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQA
EETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFIS
QEIRAAEDPEFETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL
Sequence of entity 5 (E, e), FASTA
>7YQ2_5 Cytochrome b559 subunit alpha (chains E, e)
MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQ
RSIPLVTDRFEAKQQVETFLEQLK
Sequence of entity 6 (F, f), FASTA
>7YQ2_6 Cytochrome b559 subunit beta (chains F, f)
MTSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR
Sequence of entity 7 (H, h), FASTA
>7YQ2_7 Photosystem II reaction center protein H (chains H, h)
MARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNV
SWKALG
Sequence of entity 8 (I, i), FASTA
>7YQ2_8 Photosystem II reaction center protein I (chains I, i)
METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE
Sequence of entity 9 (J, j), FASTA
>7YQ2_9 Photosystem II reaction center protein J (chains J, j)
MMSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL
Sequence of entity 10 (K, k), FASTA
>7YQ2_10 Photosystem II reaction center protein K (chains K, k)
MIDALVLVAKLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR
Sequence of entity 11 (L, l), FASTA
>7YQ2_11 Photosystem II reaction center protein L (chains L, l)
MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN
Sequence of entity 12 (M, m), FASTA
>7YQ2_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
LMTDodecyl-beta-D-maltosideC24 H46 O1119
BCTBicarbonate ionC H O33
CACalcium ionCa7
HTGheptyl 1-thio-beta-D-glucopyranosideC13 H26 O5 S31
DGDDigalactosyl diacyl glycerol (DGDG)C51 H96 O1510
LHG1,2-dipalmitoyl-phosphatidyl-glyceroleC38 H75 O10 P9
HEMProtoporphyrin IX containing FEC34 H32 Fe N4 O42
RRX(3R)-beta,beta-caroten-3-olC40 H56 O2
MGMagnesium ionMg2
HECHeme CC34 H36 Fe N4 O42

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

Primary citation

Crystal structures of photosystem II from a cyanobacterium expressing psbA 2 in comparison to psbA 3 reveal differences in the D1 subunit. Nakajima, Y., Ugai-Amo, N., Tone, N. et al. J Biol Chem (2022) 298:102668-102668. DOI 10.1016/j.jbc.2022.102668 · PubMed

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