PDB entry 6rny

View 6rny on RCSB PDB site
Description: pfv intasome - nucleosome strand transfer complex
Deposited on 2019-05-09, released 2019-09-25
The last revision was dated 2019-12-18, with a file datestamp of 2019-12-13.
Experiment type: EM
Resolution: 3.9 Å
R-factor: N/A
AEROSPACI score: 0.08 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.3
    Species: Homo sapiens [TaxId:9606]
    Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Histone H2A type 1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AG, H2AFP, HIST1H2AI, H2AFC, HIST1H2AK, H2AFD, HIST1H2AL, H2AFI, HIST1H2AM, H2AFN
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Histone H2B type 1-C/E/F/G/I
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Histone H3.3
    Species: Homo sapiens [TaxId:9606]
    Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Histone H2A type 1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AG, H2AFP, HIST1H2AI, H2AFC, HIST1H2AK, H2AFD, HIST1H2AL, H2AFI, HIST1H2AM, H2AFN
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Histone H2B type 1-C/E/F/G/I
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: DNA (128-mer)
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
  • Chain 'J':
    Compound: DNA (53-mer)
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
  • Chain 'K':
    Compound: integrase
    Species: HUMAN SPUMARETROVIRUS [TaxId:11963]
    Gene: pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot P14350
      • variant (219-220)
  • Chain 'L':
    Compound: integrase
    Species: HUMAN SPUMARETROVIRUS [TaxId:11963]
    Gene: pol
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: DNA (5'-d(*ap*tp*tp*gp*tp*cp*ap*tp*gp*gp*ap*ap*tp*tp*tp*cp*gp*c)-3')
    Species: Pyrobaculum filamentous virus 1, synthetic [TaxId:1805492]
  • Chain 'O':
    Compound: integrase
    Species: HUMAN SPUMARETROVIRUS [TaxId:11963]
    Gene: pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot P14350
      • variant (219-220)
  • Chain 'P':
    Compound: integrase
    Species: HUMAN SPUMARETROVIRUS [TaxId:11963]
    Gene: pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot P14350
      • variant (220)
  • Chain 'Q':
    Compound: DNA (5'-d(*ap*tp*tp*gp*tp*cp*ap*tp*gp*gp*ap*ap*tp*tp*tp*cp*gp*c)-3')
    Species: Pyrobaculum filamentous virus 1, synthetic [TaxId:1805492]
  • Chain 'T':
    Compound: DNA (33-mer)
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
  • Chain 'U':
    Compound: DNA (108-mer)
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
  • Heterogens: MG

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:
    >6rnyA (A:)
martkqtarkstggkaprkqlatkaarksapstggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqsaaigalqeaseaylvglfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6rnyA (A:)
hryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqsaaigalqeasea
ylvglfedtnlcaihakrvtimpkdiqlarrirgera

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6rnyB (B:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6rnyB (B:)
kvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrk
tvtamdvvyalkrqgrtlygfgg

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6rnyC (C:)
msgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleylt
aeilelagnaardnkktriiprhlqlairndeelnkllgkvtiaqggvlpniqavllpkk
teshhkakgk

    Sequence, based on observed residues (ATOM records):
    >6rnyC (C:)
karakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagn
aardnkktriiprhlqlairndeelnkllgkvtiaqggvlpniqavllpk

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6rnyD (D:)
mpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysvyvykvlkqvhpdtgisskam
gimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavt
kytssk

    Sequence, based on observed residues (ATOM records):
    >6rnyD (D:)
srkesysvyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrstits
reiqtavrlllpgelakhavsegtkavtkytssk

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6rnyE (E:)
martkqtarkstggkaprkqlatkaarksapstggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqsaaigalqeaseaylvglfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6rnyE (E:)
hryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqsaaigalqeasea
ylvglfedtnlcaihakrvtimpkdiqlarrirgera

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6rnyF (F:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6rnyF (F:)
kvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrk
tvtamdvvyalkrqgrtlygfgg

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6rnyG (G:)
msgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleylt
aeilelagnaardnkktriiprhlqlairndeelnkllgkvtiaqggvlpniqavllpkk
teshhkakgk

    Sequence, based on observed residues (ATOM records):
    >6rnyG (G:)
karakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagn
aardnkktriiprhlqlairndeelnkllgkvtiaqggvlpniqavllpk

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6rnyH (H:)
mpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysvyvykvlkqvhpdtgisskam
gimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavt
kytssk

    Sequence, based on observed residues (ATOM records):
    >6rnyH (H:)
srkesysvyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrstits
reiqtavrlllpgelakhavsegtkavtkytssk

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6rnyK (K:)
gpgcntkkpnldaeldqllqghyikgypkqytyfledgkvkvsrpegvkiippqsdrqki
vlqahnlahtgreatllkianlywwpnmrkdvvkqlgrcqqclitnasnkasgpilrpdr
pqkpfdkffidyigplppsqgylyvlvvvdgmtgftwlyptkapstsatvkslnvltsia
ipkvihsdqgaaftsstfaewakergihlefstpyhpqssgkverknsdikrlltkllvg
rptkwydllpvvqlalnntyspvlkytphqllfgidsntpfanqdtldltreeelsllqe
irtslyhpstppassrswspvvgqlvqervarpaslrprwhkpstvlkvlnprtvvildh
lgnnrtvsidnlkptshqngttndtatmdhlekne

    Sequence, based on observed residues (ATOM records):
    >6rnyK (K:)
kvsrpegvkiippqsdrqkivlqahnlahtgreatllkianlywwpnmrkdvvkqlgrcq
qclitnasnkasgpilrpdrpqkpfdkffidyigplppsqgylyvlvvvdgmtgftwlyp
tkapstsatvkslnvltsiaipkvihsdqgaaftsstfaewakergihlefstpyhpqss
gkverknsdikrlltkllvgrptkwydllpvvqlalnntyspvlkytphqllfgidsntp
fanqdtldltreeelsllqeirtslyhpstppassrswspvvgqlvqervarpaslrprw
hkpstvlkvlnprtvvildhlgnnrtvsidnlkptshq

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6rnyL (L:)
gpgcntkkpnldaeldqllqghyikgypkqytyfledgkvkvsrpegvkiippqsdrqki
vlqahnlahtgreatllkianlywwpnmrkdvvkqlgrcqqclitnasnkasgpilrpdr
pqkpfdkffidyigplppsqgylyvlvvvdgmtgftwlyptkapstsatvkslnvltsia
ipkvihsdqgaaftsstfaewakergihlefstpyhpqssgkverknsdikrlltkllvg
rptkwydllpvvqlalnntyspvlkytphqllfgidsntpfanqdtldltreeelsllqe
irtslyhpstppassrswspvvgqlvqervarpaslrprwhkpstvlkvlnprtvvildh
lgnnrtvsidnlkptshqngttndtatmdhlekne

    Sequence, based on observed residues (ATOM records):
    >6rnyL (L:)
pfdkffidyigplppsqgylyvlvvvdgmtgftwlyptkapstsatvkslnvltsiaipk
vihsdqgaaftsstfaewakergihleverknsdikrlltkllvgrptkwydllpvvqla
lnntyspvlkytphqllfgid

  • Chain 'M':
    No sequence available.

  • Chain 'O':
    Sequence, based on SEQRES records:
    >6rnyO (O:)
gpgcntkkpnldaeldqllqghyikgypkqytyfledgkvkvsrpegvkiippqsdrqki
vlqahnlahtgreatllkianlywwpnmrkdvvkqlgrcqqclitnasnkasgpilrpdr
pqkpfdkffidyigplppsqgylyvlvvvdgmtgftwlyptkapstsatvkslnvltsia
ipkvihsdqgaaftsstfaewakergihlefstpyhpqssgkverknsdikrlltkllvg
rptkwydllpvvqlalnntyspvlkytphqllfgidsntpfanqdtldltreeelsllqe
irtslyhpstppassrswspvvgqlvqervarpaslrprwhkpstvlkvlnprtvvildh
lgnnrtvsidnlkptshqngttndtatmdhlekne

    Sequence, based on observed residues (ATOM records):
    >6rnyO (O:)
kvsrpegvkiippqsdrqkivlqahnlahtgreatllkianlywwpnmrkdvvkqlgrcq
qclitnasnkasgpilrpdrpqkpfdkffidyigplppsqgylyvlvvvdgmtgftwlyp
tkapstsatvkslnvltsiaipkvihsdqgaaftsstfaewakergihlefstpyhpqss
gkverknsdikrlltkllvgrptkwydllpvvqlalnntyspvlkytphqllfgidsntp
fanqdtldltreeelsllqeirtslyhpstppassrswspvvgqlvqervarpaslrprw
hkpstvlkvlnprtvvildhlgnnrtvsidnlkptshq

  • Chain 'P':
    Sequence, based on SEQRES records:
    >6rnyP (P:)
gpgcntkkpnldaeldqllqghyikgypkqytyfledgkvkvsrpegvkiippqsdrqki
vlqahnlahtgreatllkianlywwpnmrkdvvkqlgrcqqclitnasnkasgpilrpdr
pqkpfdkffidyigplppsqgylyvlvvvdgmtgftwlyptkapstsatvkslnvltsia
ipkvihsdqgaaftsstfaewakergihlefstpyhpqssgkverknsdikrlltkllvg
rptkwydllpvvqlalnntyspvlkytphqllfgidsntpfanqdtldltreeelsllqe
irtslyhpstppassrswspvvgqlvqervarpaslrprwhkpstvlkvlnprtvvildh
lgnnrtvsidnlkptshqngttndtatmdhlekne

    Sequence, based on observed residues (ATOM records):
    >6rnyP (P:)
drpqkpfdkffidyigplppsqgylyvlvvvdgmtgftwlyptkapstsatvkslnvlts
iaipkvihsdqgaaftsstfaewakergihlefsgkverknsdikrlltkllvgrptkwy
dllpvvqlalnntyspvlkytphqllfgidsntpfan

  • Chain 'Q':
    No sequence available.

  • Chain 'T':
    No sequence available.

  • Chain 'U':
    No sequence available.