PDB entry 6uri

View 6uri on RCSB PDB site
Description: HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex
Class: viral protein
Keywords: cd4, viral protein
Deposited on 2019-10-23, released 2020-07-29
The last revision prior to the SCOPe 2.07 freeze date was dated 2020-09-23, with a file datestamp of 2020-09-18.
Experiment type: XRAY
Resolution: 3 Å
R-factor: N/A
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: AP-2 complex subunit alpha
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Ap2a2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6uria_
  • Chain 'B':
    Compound: ap-2 complex subunit beta
    Species: Homo sapiens [TaxId:9606]
    Gene: AP2B1, ADTB2, CLAPB1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P63010
      • variant (39)
      • variant (444)
      • variant (457)
    Domains in SCOPe 2.07: d6urib_
  • Chain 'D':
    Compound: cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: ap-2 complex subunit mu
    Species: Homo sapiens [TaxId:9606]
    Gene: AP2M1, CLAPM1, KIAA0109
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6urim_
  • Chain 'N':
    Compound: Protein Nef
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: nef
    Database cross-references and differences (RAF-indexed):
  • Chain 'S':
    Compound: ap-2 complex subunit sigma
    Species: Homo sapiens [TaxId:9606]
    Gene: Ap2s1, Ap17, Claps2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P53680 (0-141)
      • conflict (44)
    Domains in SCOPe 2.07: d6uris_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6uriA (A:)
    mgsshhhhhhsqdpmpavskgegmrglavfisdirnckskeaeikrinkelanirskfkg
    dkaldgyskkkyvckllfifllghdidfghmeavnllssnrytekqigylfisvlvnsns
    elirlinnaikndlasrnptfmglalhcianvgsremaeafageipkilvagdtmdsvkq
    saalcllrlyrtspdlvpmgdwtsrvvhllndqhlgvvtaatslittlaqknpeefktsv
    slavsrlsrivtsastdlqdytyyfvpapwlsvkllrllqcypppedpavrgrlteclet
    ilnkaqeppkskkvqhsnaknavlfeaisliihhdsepnllvracnqlgqflqhretnlr
    ylalesmctlassefsheavkthietvinalkterdvsvrqravdllyamcdrsnaqqiv
    aemlsyletadysireeivlkvailaekyavdytwyvdtilnliriagdyvseevwyrvi
    qivinrddvqgyaaktvfealqapachenlvkvggyilgefgnliagdprsspliqfnll
    hskfhlcsvptralllstyikfvnlfpevkatiqdvlrsdsqlknadvelqqraveylrl
    stvastdilatvleemppfperessilaklkkkkgenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >6uriA (A:)
    gmrglavfisdirnckskeaeikrinkelanirskfkgdkaldgyskkkyvckllfifll
    ghdidfghmeavnllssnrytekqigylfisvlvnsnselirlinnaikndlasrnptfm
    glalhcianvgsremaeafageipkilvagdtmdsvkqsaalcllrlyrtspdlvpmgdw
    tsrvvhllndqhlgvvtaatslittlaqknpeefktsvslavsrlsrivtsastdlqdyt
    yyfvpapwlsvkllrllqcypppedpavrgrltecletilnkaqeppkskkvqhsnakna
    vlfeaisliihhdsepnllvracnqlgqflqhretnlrylalesmctlassefsheavkt
    hietvinalkterdvsvrqravdllyamcdrsnaqqivaemlsyletadysireeivlkv
    ailaekyavdytwyvdtilnliriagdyvseevwyrviqivinrddvqgyaaktvfealq
    apachenlvkvggyilgefgnliagdprsspliqfnllhskfhlcsvptralllstyikf
    vnlfpevkatiqdvlrsdsqlknadvelqqraveylrlstvastdilatvleemppfper
    essilaklkkk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6uriB (B:)
    mgsshhhhhhsqdpnsssarlqvdmtdskyfttnkkgeiselkaelnnekkekrkeavkk
    viaamtvgkdvsslfpdvvncmqtdnlelkklvylylmnyaksqpdmaimavnsfvkdce
    dpnpliralavrtmgcirvdkiteylceplrkclkdedpyvrktaavcvaklhdinaqmv
    edqgfldslrdliadsnpmvvanavaalseiseshpnsnlldlnpqninklltalnecte
    wgqifildclsnynpkddreaqsicervtprlshansavvlsavkvlmkflellpkdsdy
    ynmllkklapplvtllsgepevqyvalrninlivqkrpeilkqeikvffvkyndpiyvkl
    ekldimirlasqaniaqvlaelkeyatevdvdfvrkavraigrcaikveqsaercvstll
    dliqtkvnyvvqeaivvirdifrkhpnkyesiiatlcgnldsldepdaraamiwivgeya
    eridnadellesflegfhdestqvqltlltaivklflkkpsetqelvqqvlslatqdsdn
    pdlrdrgyiywrllstdpvtakevvlsekpliseetdlieptlldelichigslasvyhk
    ppnafvegshgihrk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6uriB (B:)
    geiselkaelnnensfvkdcedpnpliralavrtmgcirvdkieplrkclkdedpyvrkt
    aavcvaklhdinaqrdliadsnpmvvanavaalseisnpqninklltalnectewgqifi
    ldclsnynpkddreaqsicervtprlshansavvlsavkvlmkflellpkdsdyynmllk
    klapplvtllsgepevqyvalrninlivqkrpeilkqeikvffvkyndpiyvklekldim
    irlasqaniaqvlaelkeyatevdvdfvrkavraigrcaikveqsaercvstlldliqtk
    vnyvvqeaivvirdifrkhpnkyesiiatlcgnldsldepdaraamiwivgeyaeridna
    dellesflegfhdestqvqltlltaivklflkkpsetqelvqqvlslatqdsdnpdlrdr
    gyiywrllstdpvtakevvlsekpliseetdlieptlldelichigslasvyhkppnafv
    

  • Chain 'D':
    No sequence available.

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >6uriM (M:)
    migglfiynhkgevlisrvyrddigrnavdafrvnviharqqvrspvtniartsffhvkr
    sniwlaavtkqnvnaamvfeflykmcdvmaayfgkiseeniknnfvliyelldeildfgy
    pqnsetgalktfitq
    

    Sequence, based on observed residues (ATOM records): (download)
    >6uriM (M:)
    migglfiynhkgevlisrvyrddigrnavdafrvnvihvrspvtniartsffhvkrsniw
    laavtkqnvnaamvfeflykmcdvmaayfgkiseeniknnfvliyelldeildfgypqns
    

  • Chain 'N':
    No sequence available.

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6uriS (S:)
    mirfiliqnragktrlakwymqfdddekqklieevhavvtvrdarhtnfvefrnfkiiyr
    ryaglyfcicvdvndnnlayleaihnfvevlneyfhnvceldlvfnfykvytvvdemfla
    geiretsqtkvlkqllmlqsle