PDB entry 4ub8

View 4ub8 on RCSB PDB site
Description: Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser
Class: electron transport, photosynthesis
Keywords: photosynthesis, ELECTRON TRANSPORT, 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: d4ub8a_
  • Chain 'B':
    Compound: Photosystem II CP47 chlorophyll apoprotein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8b_
  • 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: d4ub8c_
  • Chain 'D':
    Compound: Photosystem II D2 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8d_
  • Chain 'E':
    Compound: Cytochrome b559 subunit alpha
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8e_
  • Chain 'F':
    Compound: Cytochrome b559 subunit beta
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8f_
  • Chain 'H':
    Compound: Photosystem II reaction center protein H
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8h_
  • Chain 'I':
    Compound: Photosystem II reaction center protein I
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8i_
  • Chain 'J':
    Compound: Photosystem II reaction center protein J
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8j_
  • 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: d4ub8k_
  • Chain 'L':
    Compound: Photosystem II reaction center protein L
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8l_
  • 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: d4ub8m_
  • Chain 'O':
    Compound: Photosystem II manganese-stabilizing polypeptide
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8o_
  • Chain 'R':
    Compound: Photosystem II protein Y
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'T':
    Compound: Photosystem II reaction center protein T
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • 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: d4ub8u_
  • Chain 'V':
    Compound: cytochrome c-550
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8v_
  • Chain 'X':
    Compound: Photosystem II reaction center protein X
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8x_
  • Chain 'Y':
    Compound: Photosystem II reaction center protein ycf12
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Z':
    Compound: Photosystem II reaction center protein Z
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ub8z_
  • 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):
  • 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):
  • Chain 'e':
    Compound: Cytochrome b559 subunit alpha
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'f':
    Compound: Cytochrome b559 subunit beta
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'h':
    Compound: Photosystem II reaction center protein H
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'i':
    Compound: Photosystem II reaction center protein I
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'j':
    Compound: Photosystem II reaction center protein J
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • 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):
  • 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):
  • Chain 't':
    Compound: Photosystem II reaction center protein T
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • 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):
  • Chain 'x':
    Compound: Photosystem II reaction center protein X
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'y':
    Compound: Photosystem II reaction center protein ycf12
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'z':
    Compound: Photosystem II reaction center protein Z
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Heterogens: FE2, CL, BCT, CLA, PHO, BCR, SQD, GOL, UNL, LMT, OEX, PL9, CA, LMG, HTG, DGD, LHG, HEM, MG, HEC, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4ub8A (A:)
    mtttlqrresanlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdi
    dgirepvsgsllygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfl
    lgascymgrqwelsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtf
    nfmivfqaehnilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfg
    qeeetynivaahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngf
    nfnhsvidakgnvintwadiinranlgmevmhernahnfpldla
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8A (A:)
    anlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdidgirepvsgs
    llygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfllgascymgrq
    welsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtfnfmivfqaeh
    nilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfgqeeetyniva
    ahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngfnfnhsvidak
    gnvintwadiinranlgmevmhernahnfpldla
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4ub8B (B:)
    glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
    vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
    lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
    apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
    iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
    wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
    ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
    rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
    idpelspeqvewgfyqkvgdvttrk
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8B (B:)
    glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
    vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
    lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
    apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
    iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
    wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
    ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
    rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
    idpelspeqvewgfyqkvgdvttr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4ub8C (C:)
    nsifatnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipe
    kpmyeqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpe
    tleeyssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrv
    itnptldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfg
    warrafiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtfl
    irdqklganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldln
    kikndiqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlafffl
    vghlwhagraraaaagfekgidresepvlsmpsld
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8C (C:)
    atnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipekpmy
    eqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpetlee
    yssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrvitnp
    tldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfgwarr
    afiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtflirdq
    klganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldlnkikn
    diqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlaffflvghl
    whagraraaaagfekgidresepvlsmpsld
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4ub8D (D:)
    ergwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassyleg
    cnfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqf
    eiarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhn
    wtlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtan
    rfwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpe
    fetfytknlllnegirawmapqdqphenfvfpeevlprgnal
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4ub8E (E:)
    magttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeq
    rsiplvtdrfeakqqvetfleqlk
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8E (E:)
    ttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeqrsi
    plvtdrfeakqqvetfleqlk
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4ub8F (F:)
    tsntpnqepvsypiftvrwvavhtlavptifflgaiaamqfiqr
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8F (F:)
    sypiftvrwvavhtlavptifflgaiaamqfiqr
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4ub8H (H:)
    arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
    wkalg
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4ub8I (I:)
    metlkitvyivvtffvllfvfgflsgdparnpkrkdle
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >4ub8J (J:)
    mseggriplwivatvagmgvivivglffygayaglgssl
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8J (J:)
    seggriplwivatvagmgvivivglffygayaglgssl
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4ub8K (K:)
    klpeayaifdplvdvlpvipvlflalafvwqaavgfr
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4ub8L (L:)
    mepnpnrqpvelnrtslylglllilvlallfssyffn
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >4ub8M (M:)
    mevnqlgliatalfvlvpsvfliilyvqtesqqkss
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8M (M:)
    mevnqlgliatalfvlvpsvfliilyvqtesqqk
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >4ub8O (O:)
    qtltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqe
    aefvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftv
    knlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeel
    aranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyas
    iepa
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8O (O:)
    tltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqea
    efvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftvk
    nlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeela
    ranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyasi
    epa
    

  • Chain 'R':
    No sequence available.

  • Chain 'T':
    No sequence available.

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >4ub8U (U:)
    atasteeelvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesved
    vlnipglterqkqilrenlehftvtevetalveggdrynnglyk
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8U (U:)
    elvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesvedvlnipgl
    terqkqilrenlehftvtevetalveggdrynnglyk
    

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4ub8V (V:)
    aeltpevltvplnsegktitltekqylegkrlfqyacaschvggitktnpsldlrtetla
    latpprdnieglvdymknpttydgeqeiaevhpslrsadifpkmrnltekdlvaiaghil
    vepkilgdkwgggkvyy
    

  • Chain 'X':
    Sequence, based on SEQRES records: (download)
    >4ub8X (X:)
    titpslkgffigllsgavvlgltfavliaisqidkvqrsl
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ub8X (X:)
    titpslkgffigllsgavvlgltfavliaisqidkvqrs
    

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4ub8Z (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.