SCOPe 2.08: Structural Classification of Proteins

PDB entry 6jln

View 6jln on RCSB PDB site
Description: XFEL structure of cyanobacterial photosystem II (1F 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: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.22 (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)
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 (4-454)
Domains in SCOPe 2.08: d6jlnc_
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)
Domains in SCOPe 2.08: d6jlne_
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)
Domains in SCOPe 2.08: d6jlnh_
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: d6jlni_
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)
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):
- Uniprot P12241 (0-36)
Domains in SCOPe 2.08: d6jlnl_
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: d6jlnm_
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: d6jlno_
Chain 'R':
Compound: Photosystem II protein Y
Species: Thermosynechococcus vulcanus [TaxId:32053]
Database cross-references and differences (RAF-indexed):
- Uniprot P0DM37 (0-End)
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: d6jlnt_
Chain 'U':
Compound: Photosystem II 12 kDa extrinsic protein
Species: Thermosynechococcus vulcanus [TaxId:32053]
Database cross-references and differences (RAF-indexed):
- Uniprot P56152 (Start-103)
Domains in SCOPe 2.08: d6jlnu_
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: d6jlnv_
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: d6jlnx_
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)
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: d6jlna_
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 2.08: d6jlnb_
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)
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 2.08: d6jlnd_
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)
Domains in SCOPe 2.08: d6jlnf_
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)
Domains in SCOPe 2.08: d6jlnj_
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: d6jlnk_
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)
  - see sequence details (7)
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):
- Uniprot P56152 (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)
Domains in SCOPe 2.08: d6jlnz_
Heterogens: FE2, CL, BCT, CLA, PHO, BCR, SQD, GOL, LMT, OEX, OEY, PL9, UNL, LMG, CA, HTG, DGD, LHG, HEM, MG, HOH

PDB Chain Sequences:

Chain 'A':
No sequence available.
Chain 'B':
No sequence available.

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

>6jlnC (C:)
nsifatnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipe
kpmyeqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpe
tleeyssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrv
itnptldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfg
warrafiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtfl
irdqklganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldln
kikndiqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlafffl
vghlwhagraraaaagfekgidresepvlsmpsld

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

>6jlnC (C:)
atnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipekpmy
eqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpetlee
yssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrvitnp
tldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfgwarr
afiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtflirdq
klganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldlnkikn
diqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlaffflvghl
whagraraaaagfekgidresepvlsmpsld

Chain 'D':
No sequence available.

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

>6jlnE (E:)
magttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeq
rsiplvtdrfeakqqvetfleqlk

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

>6jlnE (E:)
ttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeqrsi
plvtdrfeakqqvetfleqlk

Chain 'F':
No sequence available.

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

>6jlnH (H:)
arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
wkalg

Chain 'I':
Sequence; same for both SEQRES and ATOM records: (download)
```
>6jlnI (I:)
metlkitvyivvtffvllfvfgflsgdparnpkrkdle
```
Chain 'J':
No sequence available.
Chain 'K':
No sequence available.
Chain 'L':
Sequence; same for both SEQRES and ATOM records: (download)
```
>6jlnL (L:)
mepnpnrqpvelnrtslylglllilvlallfssyffn
```
Chain 'M':
Sequence, based on SEQRES records: (download)
```
>6jlnM (M:)
mevnqlgliatalfvlvpsvfliilyvqtesqqkss
```
Sequence, based on observed residues (ATOM records): (download)
```
>6jlnM (M:)
mevnqlgliatalfvlvpsvfliilyvqtesqqk
```

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

>6jlnO (O:)
qtltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqe
aefvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftv
knlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeel
aranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyas
iepa

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

>6jlnO (O:)
tltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqea
efvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftvk
nlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeela
ranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyasi
epa

Chain 'R':
No sequence available.
Chain 'T':
Sequence, based on SEQRES records: (download)
```
>6jlnT (T:)
metityvfifaciialfffaiffreppritkk
```
Sequence, based on observed residues (ATOM records): (download)
```
>6jlnT (T:)
metityvfifaciialfffaiffrepprit
```

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

>6jlnU (U:)
atasteeelvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesved
vlnipglterqkqilrenlehftvtevetalveggdrynnglyk

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

>6jlnU (U:)
elvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesvedvlnipgl
terqkqilrenlehftvtevetalveggdrynnglyk

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

>6jlnV (V:)
aeltpevltvplnsegktitltekqylegkrlfqyacaschvggitktnpsldlrtetla
latpprdnieglvdymknpttydgeqeiaevhpslrsadifpkmrnltekdlvaiaghil
vepkilgdkwgggkvyy

Chain 'X':
Sequence, based on SEQRES records: (download)
```
>6jlnX (X:)
titpslkgffigllsgavvlgltfavliaisqidkvqrsl
```
Sequence, based on observed residues (ATOM records): (download)
```
>6jlnX (X:)
titpslkgffigllsgavvlgltfavliaisqidkvqrs
```
Chain 'Y':
No sequence available.
Chain 'Z':
No sequence available.

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

>6jlna (a:)
mtttlqrresanlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdi
dgirepvsgsllygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfl
lgascymgrqwelsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtf
nfmivfqaehnilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfg
qeeetynivaahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngf
nfnhsvidakgnvintwadiinranlgmevmhernahnfpldla

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

>6jlna (a:)
anlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdidgirepvsgs
llygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfllgascymgrq
welsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtfnfmivfqaeh
nilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfgqeeetyniva
ahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngfnfnhsvidak
gnvintwadiinranlgmevmhernahnfpldla

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

>6jlnb (b:)
glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
idpelspeqvewgfyqkvgdvttrk

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

>6jlnb (b:)
glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
idpelspeqvewgfyqkvgdvtt

Chain 'c':
No sequence available.

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

>6jlnd (d:)
ergwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassyleg
cnfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqf
eiarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhn
wtlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtan
rfwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpe
fetfytknlllnegirawmapqdqphenfvfpeevlprgnal

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

>6jlnd (d:)
rgwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassylegc
nfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqfe
iarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhnw
tlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtanr
fwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpef
etfytknlllnegirawmapqdqphenfvfpeevlprgnal

Chain 'e':
No sequence available.
Chain 'f':
Sequence, based on SEQRES records: (download)
```
>6jlnf (f:)
tsntpnqepvsypiftvrwvavhtlavptifflgaiaamqfiqr
```
Sequence, based on observed residues (ATOM records): (download)
```
>6jlnf (f:)
piftvrwvavhtlavptifflgaiaamqfiqr
```
Chain 'h':
No sequence available.
Chain 'i':
No sequence available.
Chain 'j':
Sequence; same for both SEQRES and ATOM records: (download)
```
>6jlnj (j:)
mseggriplwivatvagmgvivivglffygayaglgssl
```
Chain 'k':
Sequence; same for both SEQRES and ATOM records: (download)
```
>6jlnk (k:)
klpeayaifdplvdvlpvipvlflalafvwqaavgfr
```
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':
Sequence; same for both SEQRES and ATOM records: (download)

>6jlnz (z:)
mtilfqlalaalvilsfvmvigvpvayaspqdwdrskqliflgsglwialvlvvgvlnff
vv