PDB entry 6r8y

View 6r8y on RCSB PDB site
Description: cryo-em structure of ncp-6-4pp(-1)-uv-ddb
Deposited on 2019-04-02, released 2019-06-12
The last revision was dated 2019-12-18, with a file datestamp of 2019-12-13.
Experiment type: EM
Resolution: 4.3 Å
R-factor: N/A
AEROSPACI score: 0.03 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    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-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    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-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: Human alpha-satellite DNA (145-MER)
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
  • Chain 'J':
    Compound: Human alpha-satellite DNA (145-MER) with a 6-4PP at positions 95-96
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
  • Chain 'K':
    Compound: DNA damage-binding protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: DDB1, XAP1
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: DNA damage-binding protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: DDB2
    Database cross-references and differences (RAF-indexed):

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:
    >6r8yA (A:)
gshmartkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqk
stellirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakr
vtimpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6r8yA (A:)
vkkphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqe
aceaylvglfedtnlcaihakrvtimpkdiqlarrirgera

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6r8yB (B:)
gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6r8yB (B:)
rhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteha
krktvtamdvvyalkrqgrtlygfgg

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6r8yC (C:)
gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
pkkteshhkakgk

    Sequence, based on observed residues (ATOM records):
    >6r8yC (C:)
karakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagn
aardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkkteshhk

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6r8yD (D:)
gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtk
avtkytsak

    Sequence, based on observed residues (ATOM records):
    >6r8yD (D:)
rkrsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrst
itsreiqtavrlllpgelakhavsegtkavtkytsak

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6r8yE (E:)
gshmartkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqk
stellirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakr
vtimpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6r8yE (E:)
vkkphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqe
aceaylvglfedtnlcaihakrvtimpkdiqlarrirgera

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6r8yF (F:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records):
    >6r8yF (F:)
vlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrkt
vtamdvvyalkrqgrtlygfgg

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6r8yG (G:)
gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
pkkteshhkakgk

    Sequence, based on observed residues (ATOM records):
    >6r8yG (G:)
karakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagn
aardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkkteshhk

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6r8yH (H:)
gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtk
avtkytsak

    Sequence, based on observed residues (ATOM records):
    >6r8yH (H:)
rkrsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrst
itsreiqtavrlllpgelakhavsegtkavtkytsak

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6r8yK (K:)
gggrmsynyvvtaqkptavngcvtghftsaedlnlliakntrleiyvvtaeglrpvkevg
mygkiavmelfrpkgeskdllfiltakynacileykqsgesidiitrahgnvqdrigrps
etgiigiidpecrmiglrlydglfkvipldrdnkelkafnirleelhvidvkflygcqap
ticfvyqdpqgrhvktyevslrekefnkgpwkqenveaeasmviavpepfggaiiigqes
ityhngdkylaiappiikqstivchnrvdpngsryllgdmegrlfmlllekeeqmdgtvt
lkdlrvellgetsiaecltyldngvvfvgsrlgdsqlvklnvdsneqgsyvvametftnl
gpivdmcvvdlerqgqgqlvtcsgafkegslriirngigihehasidlpgikglwplrsd
pnretddtlvlsfvgqtrvlmlngeeveetelmgfvddqqtffcgnvahqqliqitsasv
rlvsqepkalvsewkepqaknisvascnssqvvvavgralyylqihpqelrqishtemeh
evaclditplgdsnglsplcaiglwtdisarilklpsfellhkemlggeiiprsilmttf
esshyllcalgdgalfyfglnietgllsdrkkvtlgtqptvlrtfrslsttnvfacsdrp
tviyssnhklvfsnvnlkevnymcplnsdgypdslalannstltigtideiqklhirtvp
lyesprkicyqevsqcfgvlssrievqdtsggttalrpsastqalsssvsssklfsssta
phetsfgeevevhnlliidqhtfevlhahqflqneyalslvscklgkdpntyfivgtamv
ypeeaepkqgrivvfqysdgklqtvaekevkgavysmvefngkllasinstvrlyewtte
kelrtecnhynnimalylktkgdfilvgdlmrsvlllaykpmegnfeeiardfnpnwmsa
veildddnflgaenafnlfvcqkdsaattdeerqhlqevglfhlgefvnvfchgslvmqn
lgetstptqgsvlfgtvngmiglvtslseswynllldmqnrlnkviksvgkiehsfwrsf
hterktepatgfidgdliesfldisrpkmqevvanlqyddgsgmkreataddlikvveel
trih

    Sequence, based on observed residues (ATOM records):
    >6r8yK (K:)
msynyvvtaqkptavngcvtghftsaedlnlliakntrleiyvvtaeglrpvkevgmygk
iavmelfrpkgeskdllfiltakynacileykqsgesidiitrahgnvqdrigrpsetgi
igiidpecrmiglrlydglfkvipldrdnkelkafnirleelhvidvkflygcqapticf
vyqdpqgrhvktyevslrekefnkgpwkqenveaeasmviavpepfggaiiigqesityh
ngdkylaiappiikqstivchnrvdpngsryllgdmegrlfmlllekeeqmdgtvtlkdl
rvellgetsiaecltyldngvvfvgsrlgdsqlvklnvdsneqgsyvvametftnlgpiv
dmcvvdlerqgqgqlvtcsgafkegslriirngklhirtvplyesprkicyqevsqcfgv
lssrievqdtsggttalrpsastqalsssvsssklfssstaphetsfgeevevhnlliid
qhtfevlhahqflqneyalslvscklgkdpntyfivgtamvypeeaepkqgrivvfqysd
gklqtvaekevkgavysmvefngkllasinstvrlyewttekelrtecnhynnimalylk
tkgdfilvgdlmrsvlllaykpmegnfeeiardfnpnwmsaveildddnflgaenafnlf
vcqkdsaattdeerqhlqevglfhlgefvnvfchgslvmqnlgetstptqgsvlfgtvng
miglvtslseswynllldmqnrlnkviksvgkiehsfwrsfhterktepatgfidgdlie
sfldisrpkmqevvanlqyddgsgmkreataddlikvveeltrih

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6r8yL (L:)
gggrmapkkrpetqktseivlrprnkrsrsplelepeakklcakgsgpsrrcdsdclwvg
lagpqilppcrsivrtlhqhklgraswpsvqqglqqsflhtldsyrilqkaapfdrrats
lawhpthpstvavgskggdimlwnfgikdkptfikgigaggsitglkfnplntnqfyass
megttrlqdfkgnilrvfassdtiniwfcsldvsassrmvvtgdnvgnvillnmdgkelw
nlrmhkkkvthvalnpccdwflatasvdqtvkiwdlrqvrgkasflyslphrhpvnaacf
spdgarllttdqkseirvysasqwdcplgliphphrhfqhltpikaawhprynlivvgry
pdpnfksctpyelrtidvfdgnsgkmmcqlydpessgisslnefnpmgdtlasamgyhil
iwsqeeartrk

    Sequence, based on observed residues (ATOM records):
    >6r8yL (L:)
vglagpqilppcrsivrtlhqhklgraswpsvqqglqqsflhtldsyrilqkaapfdrra
tslawhpthpstvavgskggdimlwnfgikdkptfikgigaggsitglkfnplntnqfya
ssmegttrlqdfkgnilrvfassdtiniwfcsldvsassrmvvtgdnvgnvillnmdgke
lwnlrmhkkkvthvalnpccdwflatasvdqtvkiwdlrqvrgkasflyslphrhpvnaa
cfspdgarllttdqkseirvysasqwdcplgliphphrhfqhltpikaawhprynlivvg
rypdpnfksctpyelrtidvfdgnsgkmmcqlydpessgisslnefnpmgdtlasamgyh
iliwsqeeartrk