PDB entry 7k5y

View 7k5y on RCSB PDB site
Description: Cryo-EM structure of a chromatosome containing human linker histone H1.4
Class: nuclear protein/DNA
Keywords: chromatosome, nucleosome, linker histones, Single-chain antibody, charge-charge interaction, chromatin, NUCLEAR PROTEIN, NUCLEAR PROTEIN-DNA complex
Deposited on 2020-09-17, released 2020-11-25
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-01-20, with a file datestamp of 2021-01-15.
Experiment type: EM
Resolution: 2.76 Å
R-factor: N/A
AEROSPACI score: 0.26 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7k5ya_
  • 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): Domains in SCOPe 2.08: d7k5yb_
  • 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): Domains in SCOPe 2.08: d7k5yc_
  • Chain 'D':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7k5yd_
  • Chain 'E':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7k5ye_
  • 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): Domains in SCOPe 2.08: d7k5yf_
  • 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): Domains in SCOPe 2.08: d7k5yg_
  • Chain 'H':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7k5yh_
  • Chain 'I':
    Compound: DNA (197-mer)
    Species: Homo sapiens [TaxId:9606]
  • Chain 'J':
    Compound: DNA (197-mer)
    Species: Homo sapiens [TaxId:9606]
  • Chain 'M':
    Compound: scFv20
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K5Y
    Domains in SCOPe 2.08: d7k5ym1, d7k5ym2
  • Chain 'N':
    Compound: scFv20
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K5Y
    Domains in SCOPe 2.08: d7k5yn1, d7k5yn2
  • Chain 'U':
    Compound: Histone H1.4
    Species: Homo sapiens [TaxId:9606]
    Gene: H1-4, H1F4, HIST1H1E
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7k5yu_

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >7k5yA (A:)
martkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yA (A:)
kphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeac
eaylvglfedtnlcaihakrvtimpkdiqlarrirge

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >7k5yB (B:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yB (B:)
kvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrk
tvtamdvvyalkrqgrtlygfgg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >7k5yC (C:)
msgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleylt
aeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkk
teshhkakgk

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yC (C:)
arakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagna
ardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpk

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >7k5yD (D:)
mpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgisskam
gimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavt
kytsak

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yD (D:)
krsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrsti
tsreiqtavrlllpgelakhavsegtkavtkytsa

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >7k5yE (E:)
martkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yE (E:)
kphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeac
eaylvglfedtnlcaihakrvtimpkdiqlarrirge

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >7k5yF (F:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yF (F:)
kvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrk
tvtamdvvyalkrqgrtlygfgg

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >7k5yG (G:)
msgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleylt
aeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkk
teshhkakgk

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yG (G:)
arakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagna
ardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpk

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >7k5yH (H:)
mpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgisskam
gimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavt
kytsak

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yH (H:)
krsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrsti
tsreiqtavrlllpgelakhavsegtkavtkytsa

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >7k5yM (M:)
mksshhhhhhenlyfqsnamdikmtqspssmhaslgervtitckasqdirsylswyqqkp
wkspktliyyatsladgvpsrfsgsgsgqdfsltinnlesddtatyyclqhgespytfgs
gtkleikraggggsggggsggggsggggsmevqlqqsgpelvepgtsvkmpckasgytft
sytiqwvkqtprqglewigyiypynagtkynekfkgkatltsdkssstvymelssltsed
savyycarkssrlrstldywgqgtsvtvss

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yM (M:)
mdikmtqspssmhaslgervtitckasqdirsylswyqqkpwkspktliyyatsladgvp
srfsgsgsgqdfsltinnlesddtatyyclqhgespytfgsgtkleikevqlqqsgpelv
epgtsvkmpckasgytftsytiqwvkqtprqglewigyiypynagtkynekfkgkatlts
dkssstvymelssltsedsavyycarkssrlrstldywgqgtsvtvs

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >7k5yN (N:)
mksshhhhhhenlyfqsnamdikmtqspssmhaslgervtitckasqdirsylswyqqkp
wkspktliyyatsladgvpsrfsgsgsgqdfsltinnlesddtatyyclqhgespytfgs
gtkleikraggggsggggsggggsggggsmevqlqqsgpelvepgtsvkmpckasgytft
sytiqwvkqtprqglewigyiypynagtkynekfkgkatltsdkssstvymelssltsed
savyycarkssrlrstldywgqgtsvtvss

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yN (N:)
mdikmtqspssmhaslgervtitckasqdirsylswyqqkpwkspktliyyatsladgvp
srfsgsgsgqdfsltinnlesddtatyyclqhgespytfgsgtkleikevqlqqsgpelv
epgtsvkmpckasgytftsytiqwvkqtprqglewigyiypynagtkynekfkgkatlts
dkssstvymelssltsedsavyycarkssrlrstldywgqgtsvtvs

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >7k5yU (U:)
msetapaapaapapaektpvkkkarksagaakrkasgppvselitkavaaskersgvsla
alkkalaaagydveknnsriklglkslvskgtlvqtkgtgasgsfklnkkaasgeakpka
kkagaakakkpagaakkpkkatgaatpkksakktpkkakkpaaaagakkakspkkakaak
pkkapkspakakavkpkaakpktakpkaakpkkaaakkk

    Sequence, based on observed residues (ATOM records): (download) 
    >7k5yU (U:)
sgppvselitkavaaskersgvslaalkkalaaagydveknnsriklglkslvskgtlvq
tkgtgasgsfklnkk