PDB entry 6u8q

View 6u8q on RCSB PDB site
Description: cryoem structure of hiv-1 cleaved synaptic complex (csc) intasome
Deposited on 2019-09-05, released 2020-02-05
The last revision was dated 2020-05-27, with a file datestamp of 2020-05-22.
Experiment type: EM
Resolution: 4.67 Å
R-factor: N/A
AEROSPACI score: 0.01 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: DNA (27-mer)
    Species: Escherichia coli, synthetic [TaxId:562]
  • Chain 'F':
    Compound: DNA (25-mer)
    Species: Escherichia coli, synthetic [TaxId:562]
  • Chain 'G':
    Compound: DNA (27-mer)
    Species: Escherichia coli, synthetic [TaxId:562]
  • Chain 'H':
    Compound: DNA (25-mer)
    Species: Escherichia coli, synthetic [TaxId:562]
  • Chain 'I':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'K':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'O':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'P':
    Compound: integrase
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Heterogens: MG, DLU

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:
    >6u8qA (A:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qA (A:)
fldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcqlkgeamhgqvdcspgi
wqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvhtdngsn
ftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigqvrdqaehlktavqmav
fihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfrvyyrdsrdpvwkgpak
llwkgegavviqdnsdikvvprrkakiird

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6u8qB (B:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qB (B:)
fldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcqlkgeacspgiwqldct
hlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvhtdngsnftsttv
kaacwwagikqefgipynpqsqgviesmnkelkkiigqvrdqaehlktavqmavfihnfk
rkggiggysagerivdiiatdiqtkelqkqitkiqnfrvyyrdsrdpvwkgpakllwkge
gavviqdnsdikvvprrkakiird

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6u8qC (C:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qC (C:)
fldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcqlkgeamhgqvdcspgi
wqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvhtdngsn
ftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigqvrdqaehlktavqmav
fihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfrvyyrdsrdpvwkgpak
llwkgegavviqdnsdikvvprrkakiird

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6u8qD (D:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qD (D:)
ldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcqlkgecspgiwqldcthl
egkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvhtdngsnftsttvka
acwwagikqefgipynpqsqgviesmnkelkkiigqvrdqaehlktavqmavfihnfkrk
ggiggysagerivdiiatdiqtkelqkqitkiqnfrvyyrdsrdpvwkgpakllwkgega
vviqdnsdikvvprrkakiird

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence, based on SEQRES records:
    >6u8qI (I:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qI (I:)
cspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvht
dngsnftsttvkaacwwagikqefsmnkelkkiigqvrdqaehlktavqmavfihnfkrk
ggiggysagerivdiiatdiqtkelqkqitkiqnfrvyyrdsrdpvwkgpakllwkgega
vviqdnsdikvvprrkakiirdygkqma

  • Chain 'J':
    Sequence, based on SEQRES records:
    >6u8qJ (J:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qJ (J:)
cspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvht
dngsnftsttvkaacwwagikqefsmnkelkkiigqvrdqaehlktavqmavfihnfkrk
ggiggysagerivdiiatdiqtkelqkqitkiqnfrvyyrdsrdpvwkgpakllwkgega
vviqdnsdikvvprrkakiirdygkqma

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6u8qK (K:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qK (K:)
cspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvht
dngsnftsttvkaacwwagikqefgviesmnkelkkiigqvrdqaehlktavqmavfihn
fkrkggiggysagerivdiiatdiq

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6u8qL (L:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qL (L:)
cspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvht
dngsnftsttvkaacwwagikqefgviesmnkelkkiigqvrdqaehlktavqmavfihn
fkrkggiggysagerivdiiatdiq

  • Chain 'M':
    Sequence, based on SEQRES records:
    >6u8qM (M:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qM (M:)
cspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvht
dngsnftsttvkaacwwagikqefgviesmnkelkkiigqvrdqaehlktavqmavfihn
fkrkggiggysagerivdiiatdiqnfrvyyrdsrdpvwkgpakllwkgegavviqdnsd
ikvvprrkakiird

  • Chain 'N':
    Sequence, based on SEQRES records:
    >6u8qN (N:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qN (N:)
cspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvht
dngsnftsttvkaacwwagikqefsmnkelkkiigqvrdqaehlktavqmavfihnfkrk
ggiggysagerivdiiatdiqt

  • Chain 'O':
    Sequence, based on SEQRES records:
    >6u8qO (O:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qO (O:)
cspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvht
dngsnftsttvkaacwwagikqefsmnkelkkiigqvrdqaehlktavqmavfihnfkrk
ggiggysagerivdiiatdiqt

  • Chain 'P':
    Sequence, based on SEQRES records:
    >6u8qP (P:)
gshmpkrgrpaatevkipkprgrpplpagtnskgppdfssdeereptpvlgsgaaaagqs
raavgrkatkktdgggfldgidkaqeehekyhsnwramasdfnlppvvakeivascdkcq
lkgeamhgqvdcspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllkl
agrwpvktvhtdngsnftsttvkaacwwagikqefgipynpqsqgviesmnkelkkiigq
vrdqaehlktavqmavfihnfkrkggiggysagerivdiiatdiqtkelqkqitkiqnfr
vyyrdsrdpvwkgpakllwkgegavviqdnsdikvvprrkakiirdygkqmagddcvasr
qded

    Sequence, based on observed residues (ATOM records):
    >6u8qP (P:)
cspgiwqldcthlegkvilvavhvasgyieaevipaetgqetayfllklagrwpvktvht
dngsnftsttvkaacwwagikqefgviesmnkelkkiigqvrdqaehlktavqmavfihn
fkrkggiggysagerivdiiatdiqnfrvyyrdsrdpvwkgpakllwkgegavviqdnsd
ikvvprrkakii