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 2.08 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 2.08: 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 2.08: 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 2.08: 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 2.08: 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