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 2.07 freeze date was dated 2017-07-26, with a file datestamp of 2017-07-21.
Experiment type: XRAY
Resolution: 1.95 Å
R-factor: N/A
AEROSPACI score: 0.33 (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 2.07: d4ub8a_
  • Chain 'B':
    Compound: Photosystem II CP47 chlorophyll apoprotein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: 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 2.07: d4ub8c_
  • Chain 'D':
    Compound: Photosystem II D2 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4ub8d_
  • Chain 'E':
    Compound: Cytochrome b559 subunit alpha
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4ub8e_
  • Chain 'F':
    Compound: Cytochrome b559 subunit beta
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: d4ub8m_
  • Chain 'O':
    Compound: Photosystem II manganese-stabilizing polypeptide
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: 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 2.07: d4ub8u_
  • Chain 'V':
    Compound: cytochrome c-550
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: 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 2.07: 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 2.07: 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, 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.