PDB entry 4ub6

View 4ub6 on RCSB PDB site
Description: Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser
Class: electron transport, photosynthesis
Keywords: membrane protein, ELECTRON TRANSPORT, PHOTOSYNTHESIS, oxygen evolution, water splitting, photo system II
Deposited on 2014-08-12, released 2014-12-03
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-07-02.
Experiment type: XRAY
Resolution: 1.95 Å
R-factor: N/A
AEROSPACI score: 0.41 (click here for full SPACI score report)

Chains and heterogens:

• Chain 'A':
  Compound: Photosystem Q(B) protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • PDB 4UB6 (Start-343)
  Domains in SCOPe 2.08: d4ub6a_
• Chain 'B':
  Compound: Photosystem II CP47 chlorophyll apoprotein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR1 (0-End)
  Domains in SCOPe 2.08: d4ub6b_
• Chain 'C':
  Compound: Photosystem II 44 kDa reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • PDB 4UB6 (Start-454)
  Domains in SCOPe 2.08: d4ub6c_
• Chain 'D':
  Compound: Photosystem II D2 protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR8 (0-341)
  Domains in SCOPe 2.08: d4ub6d_
• Chain 'E':
  Compound: Cytochrome b559 subunit alpha
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12238 (Start-83)
  Domains in SCOPe 2.08: d4ub6e_
• Chain 'F':
  Compound: Cytochrome b559 subunit beta
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12239 (Start-43)
  Domains in SCOPe 2.08: d4ub6f_
• Chain 'H':
  Compound: Photosystem II reaction center protein H
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19052 (0-64)
  Domains in SCOPe 2.08: d4ub6h_
• Chain 'I':
  Compound: Photosystem II reaction center protein I
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12240 (0-37)
  Domains in SCOPe 2.08: d4ub6i_
• Chain 'J':
  Compound: Photosystem II reaction center protein J
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q7DGD4 (Start-38)
  Domains in SCOPe 2.08: d4ub6j_
• Chain 'K':
  Compound: Photosystem II reaction center protein K
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • PDB 4UB6 (0-36)
  Domains in SCOPe 2.08: d4ub6k_
• 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 2.08: d4ub6l_
• Chain 'M':
  Compound: Photosystem II reaction center protein M
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • PDB 4UB6 (0-End)
  Domains in SCOPe 2.08: d4ub6m_
• Chain 'O':
  Compound: Photosystem II manganese-stabilizing polypeptide
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR2 (Start-243)
  Domains in SCOPe 2.08: d4ub6o_
• 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)
  Domains in SCOPe 2.08: d4ub6t_
• Chain 'U':
  Compound: Photosystem II 12 kDa extrinsic protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • PDB 4UB6 (Start-103)
  Domains in SCOPe 2.08: d4ub6u_
• 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 2.08: d4ub6v_
• 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 2.08: d4ub6x_
• 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 2.08: d4ub6z_
• Chain 'a':
  Compound: Photosystem Q(B) protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • PDB 4UB6 (Start-343)
• Chain 'b':
  Compound: Photosystem II CP47 chlorophyll apoprotein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR1 (0-End)
• Chain 'c':
  Compound: Photosystem II 44 kDa reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • PDB 4UB6 (0-454)
• 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 (Start-83)
• Chain 'f':
  Compound: Cytochrome b559 subunit beta
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12239 (Start-43)
• Chain 'h':
  Compound: Photosystem II reaction center protein H
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19052 (0-64)
• Chain 'i':
  Compound: Photosystem II reaction center protein I
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12240 (0-37)
• Chain 'j':
  Compound: Photosystem II reaction center protein J
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q7DGD4 (0-38)
• Chain 'k':
  Compound: Photosystem II reaction center protein K
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • PDB 4UB6 (0-36)
• 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):
  • PDB 4UB6 (0-End)
• Chain 'o':
  Compound: Photosystem II manganese-stabilizing polypeptide
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR2 (Start-243)
• 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):
  • PDB 4UB6 (Start-103)
• 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)
• Heterogens: FE2, CL, BCT, CLA, PHO, BCR, SQD, GOL, LMT, OEX, PL9, UNL, CA, LMG, HTG, DGD, LHG, HEM, MG, HEC, HOH

PDB Chain Sequences:

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

  >4ub6A (A:)
  mtttlqrresanlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdi
  dgirepvsgsllygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfl
  lgascymgrqwelsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtf
  nfmivfqaehnilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfg
  qeeetynivaahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngf
  nfnhsvidakgnvintwadiinranlgmevmhernahnfpldla
  

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

  >4ub6A (A:)
  anlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdidgirepvsgs
  llygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfllgascymgrq
  welsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtfnfmivfqaeh
  nilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfgqeeetyniva
  ahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngfnfnhsvidak
  gnvintwadiinranlgmevmhernahnfpldla
  

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

  >4ub6B (B:)
  glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
  vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
  lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
  apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
  iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
  wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
  ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
  rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
  idpelspeqvewgfyqkvgdvttrk
  

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

  >4ub6B (B:)
  glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
  vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
  lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
  apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
  iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
  wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
  ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
  rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
  idpelspeqvewgfyqkvgdvttr
  

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

  >4ub6C (C:)
  nsifatnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipe
  kpmyeqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpe
  tleeyssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrv
  itnptldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfg
  warrafiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtfl
  irdqklganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldln
  kikndiqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlafffl
  vghlwhagraraaaagfekgidresepvlsmpsld
  

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

  >4ub6C (C:)
  atnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipekpmy
  eqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpetlee
  yssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrvitnp
  tldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfgwarr
  afiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtflirdq
  klganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldlnkikn
  diqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlaffflvghl
  whagraraaaagfekgidresepvlsmpsld
  

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

  >4ub6D (D:)
  ergwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassyleg
  cnfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqf
  eiarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhn
  wtlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtan
  rfwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpe
  fetfytknlllnegirawmapqdqphenfvfpeevlprgnal
  

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

  >4ub6E (E:)
  magttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeq
  rsiplvtdrfeakqqvetfleqlk
  

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

  >4ub6E (E:)
  ttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeqrsi
  plvtdrfeakqqvetfleqlk
  

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

  >4ub6F (F:)
  tsntpnqepvsypiftvrwvavhtlavptifflgaiaamqfiqr
  

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

  >4ub6F (F:)
  sypiftvrwvavhtlavptifflgaiaamqfiqr
  

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

  >4ub6H (H:)
  arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
  wkalg
  

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

  >4ub6I (I:)
  metlkitvyivvtffvllfvfgflsgdparnpkrkdle
  

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

  >4ub6J (J:)
  mseggriplwivatvagmgvivivglffygayaglgssl
  

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

  >4ub6J (J:)
  seggriplwivatvagmgvivivglffygayaglgssl
  

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

  >4ub6K (K:)
  klpeayaifdplvdvlpvipvlflalafvwqaavgfr
  

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

  >4ub6L (L:)
  mepnpnrqpvelnrtslylglllilvlallfssyffn
  

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

  >4ub6M (M:)
  mevnqlgliatalfvlvpsvfliilyvqtesqqkss
  

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

  >4ub6M (M:)
  mevnqlgliatalfvlvpsvfliilyvqtesqqk
  

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

  >4ub6O (O:)
  qtltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqe
  aefvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftv
  knlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeel
  aranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyas
  iepa
  

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

  >4ub6O (O:)
  tltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqea
  efvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftvk
  nlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeela
  ranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyasi
  epa
  

  
  
• Chain 'R':
  No sequence available.
  
  
• Chain 'T':
  Sequence, based on SEQRES records: (download)
  

  >4ub6T (T:)
  metityvfifaciialfffaiffreppritkk
  

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

  >4ub6T (T:)
  metityvfifaciialfffaiffrepprit
  

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

  >4ub6U (U:)
  atasteeelvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesved
  vlnipglterqkqilrenlehftvtevetalveggdrynnglyk
  

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

  >4ub6U (U:)
  elvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesvedvlnipgl
  terqkqilrenlehftvtevetalveggdrynnglyk
  

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

  >4ub6V (V:)
  aeltpevltvplnsegktitltekqylegkrlfqyacaschvggitktnpsldlrtetla
  latpprdnieglvdymknpttydgeqeiaevhpslrsadifpkmrnltekdlvaiaghil
  vepkilgdkwgggkvyy
  

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

  >4ub6X (X:)
  titpslkgffigllsgavvlgltfavliaisqidkvqrsl
  

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

  >4ub6X (X:)
  titpslkgffigllsgavvlgltfavliaisqidkvqrs
  

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

  >4ub6Z (Z:)
  mtilfqlalaalvilsfvmvigvpvayaspqdwdrskqliflgsglwialvlvvgvlnff
  vv
  

  
  
• Chain 'a':
  No sequence available.
  
  
• Chain 'b':
  No sequence available.
  
  
• Chain 'c':
  No sequence available.
  
  
• Chain 'd':
  No sequence available.
  
  
• Chain 'e':
  No sequence available.
  
  
• Chain 'f':
  No sequence available.
  
  
• Chain 'h':
  No sequence available.
  
  
• Chain 'i':
  No sequence available.
  
  
• Chain 'j':
  No sequence available.
  
  
• Chain 'k':
  No sequence available.
  
  
• Chain 'l':
  No sequence available.
  
  
• Chain 'm':
  No sequence available.
  
  
• Chain 'o':
  No sequence available.
  
  
• Chain 't':
  No sequence available.
  
  
• Chain 'u':
  No sequence available.
  
  
• Chain 'v':
  No sequence available.
  
  
• Chain 'x':
  No sequence available.
  
  
• Chain 'y':
  No sequence available.
  
  
• Chain 'z':
  No sequence available.