PDB entry 4nee

View 4nee on RCSB PDB site
Description: crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef
Class: viral protein/protein transport
Keywords: clathrin Adaptor AP-2, HIV-1 Nef, CD4 downregulation, VIRAL PROTEIN-PROTEIN TRANSPORT complex
Deposited on 2013-10-29, released 2014-01-29
The last revision prior to the SCOPe 2.07 freeze date was dated 2014-03-05, with a file datestamp of 2014-02-28.
Experiment type: XRAY
Resolution: 2.88 Å
R-factor: 0.222
AEROSPACI score: 0.18 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: ap-2 complex subunit alpha-2
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Ap17, Ap2a2, Ap2s1, Claps2
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: ap-2 complex subunit alpha-2
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Ap17, Ap2a2, Ap2s1, Claps2
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Protein Nef
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: nef
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q90VU7 (Start-154)
      • expression tag (7-13)
    Domains in SCOPe 2.07: d4neec1, d4neec2
  • Chain 'D':
    Compound: ap-2 complex subunit sigma
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Ap2s1, Ap17, Claps2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4need_
  • Chain 'E':
    Compound: Protein Nef
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: nef
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q90VU7 (Start-154)
      • expression tag (7-13)
    Domains in SCOPe 2.07: d4neee1, d4neee2
  • Chain 'F':
    Compound: ap-2 complex subunit sigma
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Ap2s1, Ap17, Claps2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4neef_
  • Chain 'G':
    Compound: ap-2 complex subunit alpha-2
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Ap17, Ap2a2, Ap2s1, Claps2
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Protein Nef
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: nef
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q90VU7 (9-154)
      • expression tag (2-7)
      • expression tag (8-13)
    Domains in SCOPe 2.07: d4neeh1, d4neeh2
  • Chain 'I':
    Compound: ap-2 complex subunit sigma
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Ap2s1, Ap17, Claps2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4neei_
  • Chain 'J':
    Compound: ap-2 complex subunit alpha-2
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Ap17, Ap2a2, Ap2s1, Claps2
    Database cross-references and differences (RAF-indexed):
  • Chain 'K':
    Compound: Protein Nef
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: nef
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q90VU7 (9-154)
      • expression tag (1-7)
      • expression tag (8-13)
    Domains in SCOPe 2.07: d4neek1, d4neek2
  • Chain 'L':
    Compound: ap-2 complex subunit sigma
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Ap2s1, Ap17, Claps2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4neel_

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4neeC (C:)
gxxxxxxxxxxxxxeeevgfpvtpqvplrpmtykaavdlshflkekggleglihsqrrqd
ildlwiyhtqgyfpdwqnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpv
slhgmddperevlewrfdsrlafhhvarelhpeyf

    Sequence, based on observed residues (ATOM records): (download) 
    >4neeC (C:)
xxxxxxxpqvplrpmtykaavdlshflkekggleglihsqrrqdildlwiyhtqgyfpdw
qnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpvslhgmddperevlewr
fdsrlafhhvarelhpeyf

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4neeD (D:)
mirfiliqnragktrlakwymqfdddekqklieevhavvtvrdakhtnfvefrnfkiiyr
ryaglyfcicvdvndnnlayleaihnfvevlneyfhnvceldlvfnfykvytvvdemfla
geiretsqtkvlkqllmlqsle

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4neeE (E:)
gxxxxxxxxxxxxxeeevgfpvtpqvplrpmtykaavdlshflkekggleglihsqrrqd
ildlwiyhtqgyfpdwqnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpv
slhgmddperevlewrfdsrlafhhvarelhpeyf

    Sequence, based on observed residues (ATOM records): (download) 
    >4neeE (E:)
xxxxxxxpqvplrpmtykaavdlshflkekggleglihsqrrqdildlwiyhtqgyfpdw
qnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpvslhgmddperevlewr
fdsrlafhhvarelhpeyf

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4neeF (F:)
mirfiliqnragktrlakwymqfdddekqklieevhavvtvrdakhtnfvefrnfkiiyr
ryaglyfcicvdvndnnlayleaihnfvevlneyfhnvceldlvfnfykvytvvdemfla
geiretsqtkvlkqllmlqsle

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >4neeH (H:)
gxxxxxxxxxxxxxeeevgfpvtpqvplrpmtykaavdlshflkekggleglihsqrrqd
ildlwiyhtqgyfpdwqnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpv
slhgmddperevlewrfdsrlafhhvarelhpeyf

    Sequence, based on observed residues (ATOM records): (download) 
    >4neeH (H:)
xxxxxxxxxxxxvplrpmtykaavdlshflkekggleglihsqrrqdildlwiyhtqgyf
pdwqnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpvslhgmddperevl
ewrfdsrlafhhvarelhpeyf

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4neeI (I:)
mirfiliqnragktrlakwymqfdddekqklieevhavvtvrdakhtnfvefrnfkiiyr
ryaglyfcicvdvndnnlayleaihnfvevlneyfhnvceldlvfnfykvytvvdemfla
geiretsqtkvlkqllmlqsle

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >4neeK (K:)
gxxxxxxxxxxxxxeeevgfpvtpqvplrpmtykaavdlshflkekggleglihsqrrqd
ildlwiyhtqgyfpdwqnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpv
slhgmddperevlewrfdsrlafhhvarelhpeyf

    Sequence, based on observed residues (ATOM records): (download) 
    >4neeK (K:)
xxxxxxxxxxxxxqvplrpmtykaavdlshflkekggleglihsqrrqdildlwiyhtqg
yfpdwqnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpvslhgmddpere
vlewrfdsrlafhhvarelhpeyf

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4neeL (L:)
mirfiliqnragktrlakwymqfdddekqklieevhavvtvrdakhtnfvefrnfkiiyr
ryaglyfcicvdvndnnlayleaihnfvevlneyfhnvceldlvfnfykvytvvdemfla
geiretsqtkvlkqllmlqsle