PDB entry 6jlm

View 6jlm on RCSB PDB site
Description: XFEL structure of cyanobacterial photosystem II (dark state, dataset2)
Class: photosynthesis
Keywords: photosystem II, photosynthesis, PSII, membrane protein
Deposited on 2019-03-06, released 2019-10-16
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: 2.35 Å
R-factor: N/A
AEROSPACI score: 0.32 (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 (Start-343)
      • see sequence details (278)
    Domains in SCOPe 2.08: d6jlma_
  • Chain 'B':
    Compound: Photosystem II CP47 reaction center protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6jlmb_
  • Chain 'C':
    Compound: Photosystem II CP43 reaction center protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • 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): Domains in SCOPe 2.08: d6jlmf_
  • 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): Domains in SCOPe 2.08: d6jlmi_
  • 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: d6jlmj_
  • 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)
      • see sequence details (23)
      • see sequence details (29)
    Domains in SCOPe 2.08: d6jlmk_
  • 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: d6jlml_
  • 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)
      • see sequence details (7)
    Domains in SCOPe 2.08: d6jlmm_
  • 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: d6jlmo_
  • 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):
  • 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): Domains in SCOPe 2.08: d6jlmx_
  • 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):
  • Chain 'a':
    Compound: Photosystem II protein D1
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P51765 (Start-343)
      • see sequence details (278)
  • Chain 'b':
    Compound: Photosystem II CP47 reaction center protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'c':
    Compound: Photosystem II CP43 reaction center protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot D0VWR7 (4-454)
      • see sequence details (0-3)
    Domains in SCOPe 2.08: d6jlmc_
  • Chain 'd':
    Compound: Photosystem II D2 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6jlmd_
  • Chain 'e':
    Compound: Cytochrome b559 subunit alpha
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6jlme_
  • 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): Domains in SCOPe 2.08: d6jlmh_
  • 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):
    • Uniprot P19054 (0-36)
      • see sequence details (23)
      • see sequence details (29)
  • 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):
    • Uniprot P12312 (0-End)
      • see sequence details (7)
  • 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): Domains in SCOPe 2.08: d6jlmt_
  • Chain 'u':
    Compound: Photosystem II 12 kDa extrinsic protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6jlmu_
  • Chain 'v':
    Compound: cytochrome c-550
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6jlmv_
  • 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): Domains in SCOPe 2.08: d6jlmz_
  • Heterogens: FE2, CL, BCT, CLA, PHO, BCR, SQD, GOL, LMT, OEX, PL9, UNL, LMG, CA, HTG, LHG, DGD, HEM, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6jlmA (A:)
    mtttlqrresanlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdi
    dgirepvsgsllygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfl
    lgascymgrqwelsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtf
    nfmivfqaehnilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfg
    qeeetynivaahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngf
    nfnhsvidakgnvintwadiinranlgmevmhernahnfpldla
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmA (A:)
    anlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdidgirepvsgs
    llygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfllgascymgrq
    welsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtfnfmivfqaeh
    nilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfgqeeetyniva
    ahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngfnfnhsvidak
    gnvintwadiinranlgmevmhernahnfpldla
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6jlmB (B:)
    glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
    vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
    lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
    apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
    iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
    wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
    ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
    rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
    idpelspeqvewgfyqkvgdvttrk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmB (B:)
    glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
    vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
    lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
    apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
    iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
    wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
    ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
    rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
    idpelspeqvewgfyqkvgdvttr
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6jlmF (F:)
    tsntpnqepvsypiftvrwvavhtlavptifflgaiaamqfiqr
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmF (F:)
    sypiftvrwvavhtlavptifflgaiaamqfiqr
    

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6jlmI (I:)
    metlkitvyivvtffvllfvfgflsgdparnpkrkdle
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >6jlmJ (J:)
    mseggriplwivatvagmgvivivglffygayaglgssl
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmJ (J:)
    seggriplwivatvagmgvivivglffygayaglgssl
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6jlmK (K:)
    klpeayaifdplvdvlpvipvlflalafvwqaavgfr
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6jlmL (L:)
    mepnpnrqpvelnrtslylglllilvlallfssyffn
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >6jlmM (M:)
    mevnqlgliatalfvlvpsvfliilyvqtesqqkss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmM (M:)
    mevnqlgliatalfvlvpsvfliilyvqtesqqk
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >6jlmO (O:)
    qtltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqe
    aefvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftv
    knlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeel
    aranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyas
    iepa
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmO (O:)
    tltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqea
    efvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftvk
    nlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeela
    ranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyasi
    epa
    

  • Chain 'R':
    No sequence available.

  • Chain 'T':
    No sequence available.

  • Chain 'U':
    No sequence available.

  • Chain 'V':
    No sequence available.

  • Chain 'X':
    Sequence, based on SEQRES records: (download)
    >6jlmX (X:)
    titpslkgffigllsgavvlgltfavliaisqidkvqrsl
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmX (X:)
    titpslkgffigllsgavvlgltfavliaisqidkvqrs
    

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    No sequence available.

  • Chain 'a':
    No sequence available.

  • Chain 'b':
    No sequence available.

  • Chain 'c':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6jlmc (c:)
    nsifatnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipe
    kpmyeqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpe
    tleeyssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrv
    itnptldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfg
    warrafiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtfl
    irdqklganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldln
    kikndiqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlafffl
    vghlwhagraraaaagfekgidresepvlsmpsld
    

  • Chain 'd':
    Sequence, based on SEQRES records: (download)
    >6jlmd (d:)
    ergwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassyleg
    cnfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqf
    eiarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhn
    wtlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtan
    rfwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpe
    fetfytknlllnegirawmapqdqphenfvfpeevlprgnal
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmd (d:)
    rgwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassylegc
    nfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqfe
    iarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhnw
    tlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtanr
    fwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpef
    etfytknlllnegirawmapqdqphenfvfpeevlprgnal
    

  • Chain 'e':
    Sequence, based on SEQRES records: (download)
    >6jlme (e:)
    magttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeq
    rsiplvtdrfeakqqvetfleqlk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlme (e:)
    ttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeqrsi
    plvtdrfeakqqvetfleqlk
    

  • Chain 'f':
    No sequence available.

  • Chain 'h':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6jlmh (h:)
    arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
    wkalg
    

  • 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':
    Sequence, based on SEQRES records: (download)
    >6jlmt (t:)
    metityvfifaciialfffaiffreppritkk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmt (t:)
    metityvfifaciialfffaiffrepprit
    

  • Chain 'u':
    Sequence, based on SEQRES records: (download)
    >6jlmu (u:)
    atasteeelvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesved
    vlnipglterqkqilrenlehftvtevetalveggdrynnglyk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jlmu (u:)
    elvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesvedvlnipgl
    terqkqilrenlehftvtevetalveggdrynnglyk
    

  • Chain 'v':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6jlmv (v:)
    aeltpevltvplnsegktitltekqylegkrlfqyacaschvggitktnpsldlrtetla
    latpprdnieglvdymknpttydgeqeiaevhpslrsadifpkmrnltekdlvaiaghil
    vepkilgdkwgggkvyy
    

  • Chain 'x':
    No sequence available.

  • Chain 'y':
    No sequence available.

  • Chain 'z':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6jlmz (z:)
    mtilfqlalaalvilsfvmvigvpvayaspqdwdrskqliflgsglwialvlvvgvlnff
    vv