PDB entry 6vn1

View 6vn1 on RCSB PDB site
Description: A 2.8 Angstrom Cryo-EM Structure of a Glycoprotein B-Neutralizing Antibody Complex Reveals a Critical Domain for Herpesvirus Fusion Initiation
Class: viral protein/immune system
Keywords: Varicella Zoster Virus, Glycoprotein B, Neutralization, Monoclonal Antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex
Deposited on 2020-01-29, released 2020-07-15
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-09-02, with a file datestamp of 2020-08-28.
Experiment type: EM
Resolution: 2.8 Å
R-factor: N/A
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Envelope glycoprotein B
    Species: Human alphaherpesvirus 3 [TaxId:10335]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6vn1a_
  • Chain 'B':
    Compound: Envelope glycoprotein B
    Species: Human alphaherpesvirus 3 [TaxId:10335]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6vn1b_
  • Chain 'C':
    Compound: Envelope glycoprotein B
    Species: Human alphaherpesvirus 3 [TaxId:10335]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6vn1c_
  • Chain 'H':
    Compound: Human monoclonal antibody 93k variable heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VN1 (0-127)
    Domains in SCOPe 2.08: d6vn1h_
  • Chain 'I':
    Compound: Human monoclonal antibody 93k variable heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VN1 (0-127)
    Domains in SCOPe 2.08: d6vn1i_
  • Chain 'J':
    Compound: Human monoclonal antibody 93k variable heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VN1 (0-127)
    Domains in SCOPe 2.08: d6vn1j_
  • Chain 'L':
    Compound: Human monoclonal antibody 93k variable light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VN1 (0-105)
    Domains in SCOPe 2.08: d6vn1l_
  • Chain 'M':
    Compound: Human monoclonal antibody 93k variable light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VN1 (0-105)
    Domains in SCOPe 2.08: d6vn1m_
  • Chain 'N':
    Compound: Human monoclonal antibody 93k variable light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VN1 (0-105)
    Domains in SCOPe 2.08: d6vn1n_

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6vn1A (A:)
mspcgyyskwrnrdrpeyrrnlrfrrffssihpnaaagsgfngpgvfitsvtgvwlcflc
ifsmfvtavvsvspssfyeslqveptqseditrsahlgdgdeireaihksqdaetkptfy
vcppptgstivrlepprtcpdyhlgknftegiavvykeniaaykfkatvyykdvivstaw
agssytqitnryadrvpipvseitdtidkfgkcsskatyvrnnhkveafnedknpqdmpl
iaskynsvgskawhttndtymvagtpgtyrtgtsvnciieevearsifpydsfglstgdi
iymspffglrdgayrehsnyamdrfhqfegyrqrdldtrallepaarnflvtphltvgwn
wkpkrtevcslvkwrevedvvrdeyahnfrftmktlsttfisetnefnlnqihlsqcvke
earaiinriyttrynsshvrtgdiqtylarggfvvvfqpllsnslarlylqelvrentnh
spqkhptrntrsrrsvpvelranrtitttssvefamlqftydhiqehvnemlarissswc
qlqnreralwsglfpinpsalastildqrvkarilgdvisvsncpelgsdtriilqnsmr
vsgsttrcysrplisivslngsgtvegqlgtdnelimsrdllepcvanhkryflfghhyv
yyedyryvreiavhdvgmistyvdlnltllkdrefmplrvytrdelrdtglldyseiqrr
nqmhslrfydidkvvqydsgtaimqgmaqffqglgtagqavghvvlgatgallstvhgft
tflsnpfgalavgllvlaglvaaffayryvlklktspmkalyplttkglkqlpegmdpfa
ekpnatdtpieeigdsqntepsvnsgfdpdkfreaqemikymtlvsaaerqeskarkknk
tsalltsrltglalrnrrgysrvrtenvtgv

    Sequence, based on observed residues (ATOM records): (download) 
    >6vn1A (A:)
tkptfyvcppptgstivrlepprtcpdyhlgknftegiavvykeniaaykfkatvyykdv
ivstawagssytqitnryadrvpipvseitdtidkfgkcsskatyvrnnhkveafnedkn
pqdmpliaskynsvgskawhttndtymvagtpgtyrtgtsvnciieevearsifpydsfg
lstgdiiymspffglrdgayrehsnyamdrfhqfegyrqrdldtrallepaarnflvtph
ltvgwnwkpkrtevcslvkwrevedvvrdeyahnfrftmktlsttfisetnefnlnqihl
sqcvkeearaiinriyttrynsshvrtgdiqtylarggfvvvfqpllsnsnrtitttssv
efamlqftydhiqehvnemlarissswcqlqnreralwsglfpinpsalastildqrvka
rilgdvisvsncpelgsdtriilqnsmrvsgsttrcysrplisivslngsgtvegqlgtd
nelimsrdllepcvanhkryflfghhyvyyedyryvreiavhdvgmistyvdlnltllkd
refmplrvytrdelrdtglldyseiqrrnqmhslrfydidkvvq

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6vn1B (B:)
mspcgyyskwrnrdrpeyrrnlrfrrffssihpnaaagsgfngpgvfitsvtgvwlcflc
ifsmfvtavvsvspssfyeslqveptqseditrsahlgdgdeireaihksqdaetkptfy
vcppptgstivrlepprtcpdyhlgknftegiavvykeniaaykfkatvyykdvivstaw
agssytqitnryadrvpipvseitdtidkfgkcsskatyvrnnhkveafnedknpqdmpl
iaskynsvgskawhttndtymvagtpgtyrtgtsvnciieevearsifpydsfglstgdi
iymspffglrdgayrehsnyamdrfhqfegyrqrdldtrallepaarnflvtphltvgwn
wkpkrtevcslvkwrevedvvrdeyahnfrftmktlsttfisetnefnlnqihlsqcvke
earaiinriyttrynsshvrtgdiqtylarggfvvvfqpllsnslarlylqelvrentnh
spqkhptrntrsrrsvpvelranrtitttssvefamlqftydhiqehvnemlarissswc
qlqnreralwsglfpinpsalastildqrvkarilgdvisvsncpelgsdtriilqnsmr
vsgsttrcysrplisivslngsgtvegqlgtdnelimsrdllepcvanhkryflfghhyv
yyedyryvreiavhdvgmistyvdlnltllkdrefmplrvytrdelrdtglldyseiqrr
nqmhslrfydidkvvqydsgtaimqgmaqffqglgtagqavghvvlgatgallstvhgft
tflsnpfgalavgllvlaglvaaffayryvlklktspmkalyplttkglkqlpegmdpfa
ekpnatdtpieeigdsqntepsvnsgfdpdkfreaqemikymtlvsaaerqeskarkknk
tsalltsrltglalrnrrgysrvrtenvtgv

    Sequence, based on observed residues (ATOM records): (download) 
    >6vn1B (B:)
tkptfyvcppptgstivrlepprtcpdyhlgknftegiavvykeniaaykfkatvyykdv
ivstawagssytqitnryadrvpipvseitdtidkfgkcsskatyvrnnhkveafnedkn
pqdmpliaskynsvgskawhttndtymvagtpgtyrtgtsvnciieevearsifpydsfg
lstgdiiymspffglrdgayrehsnyamdrfhqfegyrqrdldtrallepaarnflvtph
ltvgwnwkpkrtevcslvkwrevedvvrdeyahnfrftmktlsttfisetnefnlnqihl
sqcvkeearaiinriyttrynsshvrtgdiqtylarggfvvvfqpllsnsnrtitttssv
efamlqftydhiqehvnemlarissswcqlqnreralwsglfpinpsalastildqrvka
rilgdvisvsncpelgsdtriilqnsmrvsgsttrcysrplisivslngsgtvegqlgtd
nelimsrdllepcvanhkryflfghhyvyyedyryvreiavhdvgmistyvdlnltllkd
refmplrvytrdelrdtglldyseiqrrnqmhslrfydidkvvq

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6vn1C (C:)
mspcgyyskwrnrdrpeyrrnlrfrrffssihpnaaagsgfngpgvfitsvtgvwlcflc
ifsmfvtavvsvspssfyeslqveptqseditrsahlgdgdeireaihksqdaetkptfy
vcppptgstivrlepprtcpdyhlgknftegiavvykeniaaykfkatvyykdvivstaw
agssytqitnryadrvpipvseitdtidkfgkcsskatyvrnnhkveafnedknpqdmpl
iaskynsvgskawhttndtymvagtpgtyrtgtsvnciieevearsifpydsfglstgdi
iymspffglrdgayrehsnyamdrfhqfegyrqrdldtrallepaarnflvtphltvgwn
wkpkrtevcslvkwrevedvvrdeyahnfrftmktlsttfisetnefnlnqihlsqcvke
earaiinriyttrynsshvrtgdiqtylarggfvvvfqpllsnslarlylqelvrentnh
spqkhptrntrsrrsvpvelranrtitttssvefamlqftydhiqehvnemlarissswc
qlqnreralwsglfpinpsalastildqrvkarilgdvisvsncpelgsdtriilqnsmr
vsgsttrcysrplisivslngsgtvegqlgtdnelimsrdllepcvanhkryflfghhyv
yyedyryvreiavhdvgmistyvdlnltllkdrefmplrvytrdelrdtglldyseiqrr
nqmhslrfydidkvvqydsgtaimqgmaqffqglgtagqavghvvlgatgallstvhgft
tflsnpfgalavgllvlaglvaaffayryvlklktspmkalyplttkglkqlpegmdpfa
ekpnatdtpieeigdsqntepsvnsgfdpdkfreaqemikymtlvsaaerqeskarkknk
tsalltsrltglalrnrrgysrvrtenvtgv

    Sequence, based on observed residues (ATOM records): (download) 
    >6vn1C (C:)
tkptfyvcppptgstivrlepprtcpdyhlgknftegiavvykeniaaykfkatvyykdv
ivstawagssytqitnryadrvpipvseitdtidkfgkcsskatyvrnnhkveafnedkn
pqdmpliaskynsvgskawhttndtymvagtpgtyrtgtsvnciieevearsifpydsfg
lstgdiiymspffglrdgayrehsnyamdrfhqfegyrqrdldtrallepaarnflvtph
ltvgwnwkpkrtevcslvkwrevedvvrdeyahnfrftmktlsttfisetnefnlnqihl
sqcvkeearaiinriyttrynsshvrtgdiqtylarggfvvvfqpllsnsnrtitttssv
efamlqftydhiqehvnemlarissswcqlqnreralwsglfpinpsalastildqrvka
rilgdvisvsncpelgsdtriilqnsmrvsgsttrcysrplisivslngsgtvegqlgtd
nelimsrdllepcvanhkryflfghhyvyyedyryvreiavhdvgmistyvdlnltllkd
refmplrvytrdelrdtglldyseiqrrnqmhslrfydidkvvq

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6vn1H (H:)
qvqlvqsgaevkkpgssvkvsckasggtfsnfaiswvrqapgqglewmgrimplfvtsty
aqkfqgrvtisadaststaymelsslrsddtamyycarditapgaaptplnfygmdvwgq
gttvtvss

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6vn1I (I:)
qvqlvqsgaevkkpgssvkvsckasggtfsnfaiswvrqapgqglewmgrimplfvtsty
aqkfqgrvtisadaststaymelsslrsddtamyycarditapgaaptplnfygmdvwgq
gttvtvss

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6vn1J (J:)
qvqlvqsgaevkkpgssvkvsckasggtfsnfaiswvrqapgqglewmgrimplfvtsty
aqkfqgrvtisadaststaymelsslrsddtamyycarditapgaaptplnfygmdvwgq
gttvtvss

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6vn1L (L:)
diqmtqspstlsasvgdrvtitcrasqtistwlawyqqtprkapklmiykasilengvps
rfsgsgsgteftltisslqpedfatyycqqyksypwtfgqgtkvei

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6vn1M (M:)
diqmtqspstlsasvgdrvtitcrasqtistwlawyqqtprkapklmiykasilengvps
rfsgsgsgteftltisslqpedfatyycqqyksypwtfgqgtkvei

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6vn1N (N:)
diqmtqspstlsasvgdrvtitcrasqtistwlawyqqtprkapklmiykasilengvps
rfsgsgsgteftltisslqpedfatyycqqyksypwtfgqgtkvei