PDB entry 7d1u

View 7d1u on RCSB PDB site
Description: Cryo-EM Structure of PSII at 2.08 angstrom resolution
Class: photosynthesis
Keywords: Photosystem II, PHOTOSYNTHESIS
Deposited on 2020-09-15, released 2021-03-31
The last revision prior to the SCOPe 2.07 freeze date was dated 2021-04-07, with a file datestamp of 2021-04-02.
Experiment type: EM
Resolution: 2.08 Å
R-factor: N/A
AEROSPACI score: 0.36 (click here for full SPACI score report)

Chains and heterogens:

• Chain 'A':
  Compound: Photosystem II protein D1
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P51765 (0-333)
    • conflict (268)
• Chain 'B':
  Compound: Photosystem II CP47 reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR1 (0-End)
• Chain 'C':
  Compound: Photosystem II CP43 reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR7 (0-450)
  Domains in SCOPe 2.07: d7d1uc_
• Chain 'D':
  Compound: Photosystem II D2 protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR8 (Start-341)
  Domains in SCOPe 2.07: d7d1ud_
• Chain 'E':
  Compound: Cytochrome b559 subunit alpha
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12238 (0-80)
• Chain 'F':
  Compound: Cytochrome b559 subunit beta
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12239 (0-33)
• Chain 'H':
  Compound: Photosystem II reaction center protein H
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19052 (0-62)
• Chain 'I':
  Compound: Photosystem II reaction center protein I
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12240 (0-35)
• Chain 'J':
  Compound: Photosystem II reaction center protein J
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q7DGD4 (Start-36)
  Domains in SCOPe 2.07: d7d1uj_
• Chain 'K':
  Compound: Photosystem II reaction center protein K
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19054 (0-36)
    • conflict (23)
    • conflict (29)
  Domains in SCOPe 2.07: d7d1uk_
• Chain 'L':
  Compound: Photosystem II reaction center protein L
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12241 (0-36)
  Domains in SCOPe 2.07: d7d1ul_
• Chain 'M':
  Compound: Photosystem II reaction center protein M
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12312 (0-End)
    • conflict (7)
• Chain 'O':
  Compound: Photosystem II manganese-stabilizing polypeptide
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR2 (0-243)
  Domains in SCOPe 2.07: d7d1uo_
• Chain 'R':
  Compound: Photosystem II protein Y
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0DM37 (0-33)
• Chain 'T':
  Compound: Photosystem II reaction center protein T
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12313 (0-End)
• Chain 'U':
  Compound: Photosystem II 12 kDa extrinsic protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P56152 (0-96)
  Domains in SCOPe 2.07: d7d1uu_
• Chain 'V':
  Compound: cytochrome c-550
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A387 (0-136)
• Chain 'X':
  Compound: Photosystem II reaction center protein X
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR4 (0-End)
• Chain 'Y':
  Compound: Photosystem II reaction center protein ycf12
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR3 (Start-29)
• Chain 'Z':
  Compound: Photosystem II reaction center protein Z
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR5 (0-61)
  Domains in SCOPe 2.07: d7d1uz_
• Chain 'a':
  Compound: Photosystem II protein D1
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P51765 (0-333)
    • conflict (268)
  Domains in SCOPe 2.07: d7d1ua_
• Chain 'b':
  Compound: Photosystem II CP47 reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR1 (0-End)
  Domains in SCOPe 2.07: d7d1ub_
• Chain 'c':
  Compound: Photosystem II CP43 reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR7 (0-450)
• Chain 'd':
  Compound: Photosystem II D2 protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR8 (Start-341)
• Chain 'e':
  Compound: Cytochrome b559 subunit alpha
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12238 (0-80)
  Domains in SCOPe 2.07: d7d1ue_
• Chain 'f':
  Compound: Cytochrome b559 subunit beta
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12239 (0-33)
  Domains in SCOPe 2.07: d7d1uf_
• Chain 'h':
  Compound: Photosystem II reaction center protein H
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19052 (0-62)
  Domains in SCOPe 2.07: d7d1uh_
• Chain 'i':
  Compound: Photosystem II reaction center protein I
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12240 (0-35)
• Chain 'j':
  Compound: Photosystem II reaction center protein J
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q7DGD4 (Start-36)
• Chain 'k':
  Compound: Photosystem II reaction center protein K
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19054 (0-36)
    • conflict (23)
    • conflict (29)
• Chain 'l':
  Compound: Photosystem II reaction center protein L
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12241 (0-36)
• Chain 'm':
  Compound: Photosystem II reaction center protein M
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12312 (0-End)
    • conflict (7)
  Domains in SCOPe 2.07: d7d1um_
• Chain 'o':
  Compound: Photosystem II manganese-stabilizing polypeptide
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR2 (0-243)
• Chain 'r':
  Compound: Photosystem II protein Y
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0DM37 (0-33)
• Chain 't':
  Compound: Photosystem II reaction center protein T
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12313 (0-End)
• Chain 'u':
  Compound: Photosystem II 12 kDa extrinsic protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P56152 (0-96)
• Chain 'v':
  Compound: cytochrome c-550
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A387 (0-136)
  Domains in SCOPe 2.07: d7d1uv_
• Chain 'x':
  Compound: Photosystem II reaction center protein X
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR4 (0-End)
  Domains in SCOPe 2.07: d7d1ux_
• Chain 'y':
  Compound: Photosystem II reaction center protein ycf12
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR3 (Start-29)
• Chain 'z':
  Compound: Photosystem II reaction center protein Z
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR5 (0-61)
• Heterogens: OEX, FE2, CL, CLA, PHO, BCR, SQD, PL9, UNL, BCT, LMG, LHG, DGD, HEM, RRX, LMT, MG, HEC, HOH

PDB Chain Sequences:

• Chain 'A':
  No sequence available.
  
  
• Chain 'B':
  No sequence available.
  
  
• Chain 'C':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1uC (C:)
  atnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipekpmy
  eqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpetlee
  yssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrvitnp
  tldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfgwarr
  afiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtflirdq
  klganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldlnkikn
  diqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlaffflvghl
  whagraraaaagfekgidresepvlsmpsld
  

  
  
• Chain 'D':
  Sequence, based on SEQRES records: (download)
  

  >7d1uD (D:)
  ergwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassyleg
  cnfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqf
  eiarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhn
  wtlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtan
  rfwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpe
  fetfytknlllnegirawmapqdqpxenfvfpeevlprgnal
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >7d1uD (D:)
  rgwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassylegc
  nfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqfe
  iarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhnw
  tlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtanr
  fwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpef
  etfytknlllnegirawmapqdqpxenfvfpeevlprgnal
  

  
  
• Chain 'E':
  No sequence available.
  
  
• Chain 'F':
  No sequence available.
  
  
• Chain 'H':
  No sequence available.
  
  
• Chain 'I':
  No sequence available.
  
  
• Chain 'J':
  Sequence, based on SEQRES records: (download)
  

  >7d1uJ (J:)
  eggriplwivatvagmgvivivglffygayaglgssl
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >7d1uJ (J:)
  ggriplwivatvagmgvivivglffygayaglgssl
  

  
  
• Chain 'K':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1uK (K:)
  klpeayaifdplvdvlpvipvlflalafvwqaavgfr
  

  
  
• Chain 'L':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1uL (L:)
  mepnpnrqpvelnrtslylglllilvlallfssyffn
  

  
  
• Chain 'M':
  No sequence available.
  
  
• Chain 'O':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1uO (O:)
  qtltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqe
  aefvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftv
  knlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeel
  aranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyas
  iepa
  

  
  
• Chain 'R':
  No sequence available.
  
  
• Chain 'T':
  No sequence available.
  
  
• Chain 'U':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1uU (U:)
  elvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesvedvlnipgl
  terqkqilrenlehftvtevetalveggdrynnglyk
  

  
  
• Chain 'V':
  No sequence available.
  
  
• Chain 'X':
  No sequence available.
  
  
• Chain 'Y':
  No sequence available.
  
  
• Chain 'Z':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1uZ (Z:)
  mtilfqlalaalvilsfvmvigvpvayaspqdwdrskqliflgsglwialvlvvgvlnff
  vv
  

  
  
• Chain 'a':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1ua (a:)
  anlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdidgirepvsgs
  llygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfllgascymgrq
  welsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtfnfmivfqaeh
  nilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfgqeeetyniva
  ahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngfnfnhsvidak
  gnvintwadiinranlgmevmhernahnfpldla
  

  
  
• Chain 'b':
  Sequence, based on SEQRES records: (download)
  

  >7d1ub (b:)
  glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
  vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
  lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
  apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
  iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
  wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
  ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
  rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
  idpelspeqvewgfyqkvgdvttrk
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >7d1ub (b:)
  glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
  vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
  lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
  apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
  iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
  wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
  ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
  rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
  idpelspeqvewgfyqkvgdvttr
  

  
  
• Chain 'c':
  No sequence available.
  
  
• Chain 'd':
  No sequence available.
  
  
• Chain 'e':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1ue (e:)
  ttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeqrsi
  plvtdrfeakqqvetfleqlk
  

  
  
• Chain 'f':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1uf (f:)
  sypiftvrwvavhtlavptifflgaiaamqfiqr
  

  
  
• Chain 'h':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1uh (h:)
  arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
  wka
  

  
  
• Chain 'i':
  No sequence available.
  
  
• Chain 'j':
  No sequence available.
  
  
• Chain 'k':
  No sequence available.
  
  
• Chain 'l':
  No sequence available.
  
  
• Chain 'm':
  Sequence, based on SEQRES records: (download)
  

  >7d1um (m:)
  mevnqlgliatalfvlvpsvfliilyvqtesqqk
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >7d1um (m:)
  mevnqlgliatalfvlvpsvfliilyvqtesqq
  

  
  
• Chain 'o':
  No sequence available.
  
  
• Chain 'r':
  No sequence available.
  
  
• Chain 't':
  No sequence available.
  
  
• Chain 'u':
  No sequence available.
  
  
• Chain 'v':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >7d1uv (v:)
  aeltpevltvplnsegktitltekqylegkrlfqyacaschvggitktnpsldlrtetla
  latpprdnieglvdymknpttydgeqeiaevhpslrsadifpkmrnltekdlvaiaghil
  vepkilgdkwgggkvyy
  

  
  
• Chain 'x':
  Sequence, based on SEQRES records: (download)
  

  >7d1ux (x:)
  titpslkgffigllsgavvlgltfavliaisqidkvqrsl
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >7d1ux (x:)
  titpslkgffigllsgavvlgltfavliaisqidkvqr
  

  
  
• Chain 'y':
  No sequence available.
  
  
• Chain 'z':
  No sequence available.