PDB entry 6gsi

View 6gsi on RCSB PDB site
Description: feline calicivirus strain f9 bound to a soluble ectodomain fragment of feline junctional adhesion molecule a - leading to assembly of a portal structure at a unique three-fold axis.
Deposited on 2018-06-14, released 2019-01-16
The last revision was dated 2019-12-18, with a file datestamp of 2019-12-13.
Experiment type: EM
Resolution: 3.75 Å
R-factor: N/A
AEROSPACI score: 0.07 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: capsid protein
    Species: Feline calicivirus strain F9 [TaxId:11981]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P27406
      • conflict (138)
      • conflict (152)
      • conflict (216)
      • conflict (267-268)
      • conflict (303)
      • conflict (318)
      • conflict (337)
      • conflict (345)
      • conflict (354)
      • conflict (356)
      • conflict (388)
      • conflict (392-393)
      • conflict (396)
      • conflict (398)
      • conflict (427-428)
      • conflict (430)
      • conflict (440-441)
      • conflict (449)
      • conflict (453)
      • conflict (456)
      • conflict (458)
      • conflict (464)
      • insertion (492)
      • conflict (493)
      • conflict (496)
      • conflict (498)
      • conflict (500)
      • conflict (502)
      • conflict (505-506)
      • conflict (509)
      • conflict (511)
      • conflict (514)
      • conflict (519-520)
      • conflict (528)
      • conflict (552)
      • conflict (635-636)
      • conflict (644)
  • Chain 'B':
    Compound: capsid protein
    Species: Feline calicivirus strain F9 [TaxId:11981]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P27406
      • conflict (138)
      • conflict (152)
      • conflict (216)
      • conflict (267-268)
      • conflict (303)
      • conflict (318)
      • conflict (337)
      • conflict (345)
      • conflict (354)
      • conflict (356)
      • conflict (388)
      • conflict (392-393)
      • conflict (396)
      • conflict (398)
      • conflict (427-428)
      • conflict (430)
      • conflict (440-441)
      • conflict (449)
      • conflict (453)
      • conflict (456)
      • conflict (458)
      • conflict (464)
      • insertion (492)
      • conflict (493)
      • conflict (496)
      • conflict (498)
      • conflict (500)
      • conflict (502)
      • conflict (505-506)
      • conflict (509)
      • conflict (511)
      • conflict (514)
      • conflict (519-520)
      • conflict (528)
      • conflict (552)
      • conflict (635-636)
      • conflict (644)
  • Chain 'C':
    Compound: capsid protein
    Species: Feline calicivirus strain F9 [TaxId:11981]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P27406
      • conflict (138)
      • conflict (152)
      • conflict (216)
      • conflict (267-268)
      • conflict (303)
      • conflict (318)
      • conflict (337)
      • conflict (345)
      • conflict (354)
      • conflict (356)
      • conflict (388)
      • conflict (392-393)
      • conflict (396)
      • conflict (398)
      • conflict (427-428)
      • conflict (430)
      • conflict (440-441)
      • conflict (449)
      • conflict (453)
      • conflict (456)
      • conflict (458)
      • conflict (464)
      • insertion (492)
      • conflict (493)
      • conflict (496)
      • conflict (498)
      • conflict (500)
      • conflict (502)
      • conflict (505-506)
      • conflict (509)
      • conflict (511)
      • conflict (514)
      • conflict (519-520)
      • conflict (528)
      • conflict (552)
      • conflict (635-636)
      • conflict (644)
  • Chain 'D':
    Compound: capsid protein
    Species: Feline calicivirus strain F9 [TaxId:11981]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P27406
      • conflict (138)
      • conflict (152)
      • conflict (216)
      • conflict (267-268)
      • conflict (303)
      • conflict (318)
      • conflict (337)
      • conflict (345)
      • conflict (354)
      • conflict (356)
      • conflict (388)
      • conflict (392-393)
      • conflict (396)
      • conflict (398)
      • conflict (427-428)
      • conflict (430)
      • conflict (440-441)
      • conflict (449)
      • conflict (453)
      • conflict (456)
      • conflict (458)
      • conflict (464)
      • insertion (492)
      • conflict (493)
      • conflict (496)
      • conflict (498)
      • conflict (500)
      • conflict (502)
      • conflict (505-506)
      • conflict (509)
      • conflict (511)
      • conflict (514)
      • conflict (519-520)
      • conflict (528)
      • conflict (552)
      • conflict (635-636)
      • conflict (644)
  • Chain 'E':
    Compound: Junctional adhesion molecule A
    Species: Felis catus [TaxId:9685]
    Gene: F11R, JAM1
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Junctional adhesion molecule A
    Species: Felis catus [TaxId:9685]
    Gene: F11R, JAM1
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Junctional adhesion molecule A
    Species: Felis catus [TaxId:9685]
    Gene: F11R, JAM1
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Junctional adhesion molecule A
    Species: Felis catus [TaxId:9685]
    Gene: F11R, JAM1
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: vp2
    Species: Feline calicivirus strain F9 [TaxId:11981]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P28711
      • conflict (36)
      • conflict (38-39)
      • conflict (42)
      • conflict (84)
  • Chain 'J':
    Compound: vp2
    Species: Feline calicivirus strain F9 [TaxId:11981]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P28711 (Start-105)
      • conflict (36)
      • conflict (38-39)
      • conflict (42)
      • conflict (84)
      • conflict (100)
      • conflict (105)
  • Chain 'K':
    Compound: vp2
    Species: Feline calicivirus strain F9 [TaxId:11981]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P28711
      • conflict (36)
      • conflict (38-39)
      • conflict (42)
      • conflict (84)
  • Chain 'L':
    Compound: vp2
    Species: Feline calicivirus strain F9 [TaxId:11981]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P28711 (Start-105)
      • conflict (36)
      • conflict (38-39)
      • conflict (42)
      • conflict (84)
      • conflict (100)
      • conflict (105)
  • Heterogens: K

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6gsiA (A:)
mcstcanvlkyynwdphfrlvidpnkflsvgfcdnplmccypellpefgtvwdcdqsplq
iylesilgddewastyeaidpavppmhwdaagkifqphpgvlmhhligevakawdpnlpm
frleadgdgsitapeqgtpvggviaepsaqmsaaadmatgksvdseweaffsfhtsvnws
tsetqgkilfkqslgpllnpylehlaklyvawsgsidvrfsisgsgvfggklaaivvppg
vdpvqstsmlqyphvlfdarqvepvifsipdlrstlyhlmsdtdttslvimvyndlinpy
andsnssgcivtvetkpgadfkfhllkppgsmlthgsvpsdlipkssslwignrhwtdit
dfvirpfvfqanrhfdfnqetagwstpryrpititisekngaklgigvatdyivpgipdg
wpdttipekltpagdyaitnksgndittaagydgadvivnntnfkgmyicgslqrawgdk
kisntafittatkvdnaiepsnvidmtkiavyqdthvgkevqtsddtlsllgytgigeqa
igsdrdrvvrisvlpetgarggnhpifyknsiklgyvirsidvfnsqilhtsrqlslnhy
llppdsfavyriidsngswfdigidsdgfsfvgvssigklefpltasymgiqlakirlas
nirssmtkl

    Sequence, based on observed residues (ATOM records):
    >6gsiA (A:)
sitapeqgtpvggviaepsaqmsaaadmatgksvdseweaffsfhtsvnwstsetqgkil
fkqslgpllnpylehlaklyvawsgsidvrfsisgsgvfggklaaivvppgvdpvqstsm
lqyphvlfdarqvepvifsipdlrstlyhlmsdtdttslvimvyndlinpyandsnssgc
ivtvetkpgadfkfhllkppgsmlthgsvpsdlipkssslwignrhwtditdfvirpfvf
qanrhfdfnqetagwstpryrpititisekngaklgigvatdyivpgipdgwpdttipek
ltpagdyaitnksgndittaagydgadvivnntnfkgmyicgslqrawgdkkisntafit
tatkvdnaiepsnvidmtkiavyqdthvgkevqtsddtlsllgytgigeqaigsdrdrvv
risvlpetgarggnhpifyknsiklgyvirsidvfnsqilhtsrqlslnhyllppdsfav
yriidsngswfdigidsdgfsfvgvssigklefpltasymgiqlakirlasnir

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6gsiB (B:)
mcstcanvlkyynwdphfrlvidpnkflsvgfcdnplmccypellpefgtvwdcdqsplq
iylesilgddewastyeaidpavppmhwdaagkifqphpgvlmhhligevakawdpnlpm
frleadgdgsitapeqgtpvggviaepsaqmsaaadmatgksvdseweaffsfhtsvnws
tsetqgkilfkqslgpllnpylehlaklyvawsgsidvrfsisgsgvfggklaaivvppg
vdpvqstsmlqyphvlfdarqvepvifsipdlrstlyhlmsdtdttslvimvyndlinpy
andsnssgcivtvetkpgadfkfhllkppgsmlthgsvpsdlipkssslwignrhwtdit
dfvirpfvfqanrhfdfnqetagwstpryrpititisekngaklgigvatdyivpgipdg
wpdttipekltpagdyaitnksgndittaagydgadvivnntnfkgmyicgslqrawgdk
kisntafittatkvdnaiepsnvidmtkiavyqdthvgkevqtsddtlsllgytgigeqa
igsdrdrvvrisvlpetgarggnhpifyknsiklgyvirsidvfnsqilhtsrqlslnhy
llppdsfavyriidsngswfdigidsdgfsfvgvssigklefpltasymgiqlakirlas
nirssmtkl

    Sequence, based on observed residues (ATOM records):
    >6gsiB (B:)
peqgtpvggviaepsaqmsaaadmatgksvdseweaffsfhtsvnwstsetqgkilfkqs
lgpllnpylehlaklyvawsgsidvrfsisgsgvfggklaaivvppgvdpvqstsmlqyp
hvlfdarqvepvifsipdlrstlyhlmsdtdttslvimvyndlinpyandsnssgcivtv
etkpgadfkfhllkppgsmlthgsvpsdlipkssslwignrhwtditdfvirpfvfqanr
hfdfnqetagwstpryrpititisekngaklgigvatdyivpgipdgwpdttipekltpa
gdyaitnksgndittaagydgadvivnntnfkgmyicgslqrawgdkkisntafittatk
vdnaiepsnvidmtkiavyqdthvgkevqtsddtlsllgytgigeqaigsdrdrvvrisv
lpetgarggnhpifyknsiklgyvirsidvfnsqilhtsrqlslnhyllppdsfavyrii
dsngswfdigidsdgfsfvgvssigklefpltasymgiqlakirlasnir

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6gsiC (C:)
mcstcanvlkyynwdphfrlvidpnkflsvgfcdnplmccypellpefgtvwdcdqsplq
iylesilgddewastyeaidpavppmhwdaagkifqphpgvlmhhligevakawdpnlpm
frleadgdgsitapeqgtpvggviaepsaqmsaaadmatgksvdseweaffsfhtsvnws
tsetqgkilfkqslgpllnpylehlaklyvawsgsidvrfsisgsgvfggklaaivvppg
vdpvqstsmlqyphvlfdarqvepvifsipdlrstlyhlmsdtdttslvimvyndlinpy
andsnssgcivtvetkpgadfkfhllkppgsmlthgsvpsdlipkssslwignrhwtdit
dfvirpfvfqanrhfdfnqetagwstpryrpititisekngaklgigvatdyivpgipdg
wpdttipekltpagdyaitnksgndittaagydgadvivnntnfkgmyicgslqrawgdk
kisntafittatkvdnaiepsnvidmtkiavyqdthvgkevqtsddtlsllgytgigeqa
igsdrdrvvrisvlpetgarggnhpifyknsiklgyvirsidvfnsqilhtsrqlslnhy
llppdsfavyriidsngswfdigidsdgfsfvgvssigklefpltasymgiqlakirlas
nirssmtkl

    Sequence, based on observed residues (ATOM records):
    >6gsiC (C:)
sitapeqgtpvggviaepsaqmsaaadmatgksvdseweaffsfhtsvnwstsetqgkil
fkqslgpllnpylehlaklyvawsgsidvrfsisgsgvfggklaaivvppgvdpvqstsm
lqyphvlfdarqvepvifsipdlrstlyhlmsdtdttslvimvyndlinpyandsnssgc
ivtvetkpgadfkfhllkppgsmlthgsvpsdlipkssslwignrhwtditdfvirpfvf
qanrhfdfnqetagwstpryrpititisekngaklgigvatdyivpgipdgwpdttipek
ltpagdyaitnksgndittaagydgadvivnntnfkgmyicgslqrawgdkkisntafit
tatkvdnaiepsnvidmtkiavyqdthvgkevqtsddtlsllgytgigeqaigsdrdrvv
risvlpetgarggnhpifyknsiklgyvirsidvfnsqilhtsrqlslnhyllppdsfav
yriidsngswfdigidsdgfsfvgvssigklefpltasymgiqlakirlasnir

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6gsiD (D:)
mcstcanvlkyynwdphfrlvidpnkflsvgfcdnplmccypellpefgtvwdcdqsplq
iylesilgddewastyeaidpavppmhwdaagkifqphpgvlmhhligevakawdpnlpm
frleadgdgsitapeqgtpvggviaepsaqmsaaadmatgksvdseweaffsfhtsvnws
tsetqgkilfkqslgpllnpylehlaklyvawsgsidvrfsisgsgvfggklaaivvppg
vdpvqstsmlqyphvlfdarqvepvifsipdlrstlyhlmsdtdttslvimvyndlinpy
andsnssgcivtvetkpgadfkfhllkppgsmlthgsvpsdlipkssslwignrhwtdit
dfvirpfvfqanrhfdfnqetagwstpryrpititisekngaklgigvatdyivpgipdg
wpdttipekltpagdyaitnksgndittaagydgadvivnntnfkgmyicgslqrawgdk
kisntafittatkvdnaiepsnvidmtkiavyqdthvgkevqtsddtlsllgytgigeqa
igsdrdrvvrisvlpetgarggnhpifyknsiklgyvirsidvfnsqilhtsrqlslnhy
llppdsfavyriidsngswfdigidsdgfsfvgvssigklefpltasymgiqlakirlas
nirssmtkl

    Sequence, based on observed residues (ATOM records):
    >6gsiD (D:)
sitapeqgtpvggviaepsaqmsaaadmatgksvdseweaffsfhtsvnwstsetqgkil
fkqslgpllnpylehlaklyvawsgsidvrfsisgsgvfggklaaivvppgvdpvqstsm
lqyphvlfdarqvepvifsipdlrstlyhlmsdtdttslvimvyndlinpyandsnssgc
ivtvetkpgadfkfhllkppgsmlthgsvpsdlipkssslwignrhwtditdfvirpfvf
qanrhfdfnqetagwstpryrpititisekngaklgigvatdyivpgipdgwpdttipek
ltpagdyaitnksgndittaagydgadvivnntnfkgmyicgslqrawgdkkisntafit
tatkvdnaiepsnvidmtkiavyqdthvgkevqtsddtlsllgytgigeqaigsdrdrvv
risvlpetgarggnhpifyknsiklgyvirsidvfnsqilhtsrqlslnhyllppdsfav
yriidsngswfdigidsdgfsfvgvssigklefpltasymgiqlakirlasnir

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6gsiE (E:)
avytsepdvrvpedkpaklscsysgfsnprvewkfahgditslvcyknkitasyadrvtf
shsgitfhsvtrkdtgtytcmvsddggntygevsvqltvlvppskptvhipssatigsra
vltcsekdgsppseyywfkdgvrmplepkgnrafsnssyslnektgelvfdpvsawdtge
ytceaqngygmpmrseavrmea

    Sequence, based on observed residues (ATOM records):
    >6gsiE (E:)
vytsepdvrvpedkpaklscsysgfsnprvewkfahgditslvcyknkitasyadrvtfs
hsgitfhsvtrkdtgtytcmvsddggntygevsvqltvlvppskptvhipssatigsrav
ltcsekdgsppseyywfkdgvrmplepkgnrafsnssyslnektgelvfdpvsawdtgey
tceaqngygmpmrseavrmea

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >6gsiF (F:)
avytsepdvrvpedkpaklscsysgfsnprvewkfahgditslvcyknkitasyadrvtf
shsgitfhsvtrkdtgtytcmvsddggntygevsvqltvlvppskptvhipssatigsra
vltcsekdgsppseyywfkdgvrmplepkgnrafsnssyslnektgelvfdpvsawdtge
ytceaqngygmpmrseavrmea

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6gsiG (G:)
avytsepdvrvpedkpaklscsysgfsnprvewkfahgditslvcyknkitasyadrvtf
shsgitfhsvtrkdtgtytcmvsddggntygevsvqltvlvppskptvhipssatigsra
vltcsekdgsppseyywfkdgvrmplepkgnrafsnssyslnektgelvfdpvsawdtge
ytceaqngygmpmrseavrmea

    Sequence, based on observed residues (ATOM records):
    >6gsiG (G:)
vytsepdvrvpedkpaklscsysgfsnprvewkfahgditslvcyknkitasyadrvtfs
hsgitfhsvtrkdtgtytcmvsddggntygevsvqltvlvppskptvhipssatigsrav
ltcsekdgsppseyywfkdgvrmplepkgnrafsnssyslnektgelvfdpvsawdtgey
tceaqngygmpmrseavrme

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6gsiH (H:)
avytsepdvrvpedkpaklscsysgfsnprvewkfahgditslvcyknkitasyadrvtf
shsgitfhsvtrkdtgtytcmvsddggntygevsvqltvlvppskptvhipssatigsra
vltcsekdgsppseyywfkdgvrmplepkgnrafsnssyslnektgelvfdpvsawdtge
ytceaqngygmpmrseavrmea

    Sequence, based on observed residues (ATOM records):
    >6gsiH (H:)
avytsepdvrvpedkpaklscsysgfsnprvewkfahgditslvcyknkitasyadrvtf
shsgitfhsvtrkdtgtytcmvsddggntygevsvqltvlvppskptvhipssatigsra
vltcsekdgsppseyywfkdgvrmplepkgnrafsnssyslnektgelvfdpvsawdtge
ytceaqngygmpmrseavrm

  • Chain 'I':
    Sequence, based on SEQRES records:
    >6gsiI (I:)
mnsilglidtvtntigkaqqieldkaalgqqrelalkrmkldhqalnnqveqfnkileqr
vqgpiqsvrlaraagfrvdpysytdqnfyddqlnairlsyrnlfkn

    Sequence, based on observed residues (ATOM records):
    >6gsiI (I:)
qqieldkaalgqqrelalkrmkldhqalnnqveqfnkileqrvqgpiqsvrlaraagfrv
dpysytdqnfyddqlnairlsy

  • Chain 'J':
    Sequence, based on SEQRES records:
    >6gsiJ (J:)
mnsilglidtvtntigkaqqieldkaalgqqrelalkrmkldhqalnnqveqfnkileqr
vqgpiqsvrlaraagfrvdpysytdqnfyddqlnairlsyrnlfkn

    Sequence, based on observed residues (ATOM records):
    >6gsiJ (J:)
aqqieldkaalgqqrelalkrmkldhqalnnqveqfnkileqrvqgpiqsvrlaraagfr
vdpysytdqnfyddqlnairlsyrnlfkn

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6gsiK (K:)
mnsilglidtvtntigkaqqieldkaalgqqrelalkrmkldhqalnnqveqfnkileqr
vqgpiqsvrlaraagfrvdpysytdqnfyddqlnairlsyrnlfkn

    Sequence, based on observed residues (ATOM records):
    >6gsiK (K:)
qqieldkaalgqqrelalkrmkldhqalnnqveqfnkileqrvqgpiqsvrlaraagfrv
dpysytdqnfyddqlnairlsy

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6gsiL (L:)
mnsilglidtvtntigkaqqieldkaalgqqrelalkrmkldhqalnnqveqfnkileqr
vqgpiqsvrlaraagfrvdpysytdqnfyddqlnairlsyrnlfkn

    Sequence, based on observed residues (ATOM records):
    >6gsiL (L:)
aqqieldkaalgqqrelalkrmkldhqalnnqveqfnkileqrvqgpiqsvrlaraagfr
vdpysytdqnfyddqlnairlsyrnlfkn