PDB entry 1id3

View 1id3 on RCSB PDB site
Description: crystal structure of the yeast nucleosome core particle reveals fundamental differences in inter-nucleosome interactions
Class: structural protein/DNA
Keywords: Nucleosome Core Particle, Chromatin, Histone, Protein/DNA Interaction, Nucleoprotein, Supercoiled DNA, Complex (Nucleosome Core/DNA), STRUCTURAL PROTEIN/DNA COMPLEX
Deposited on 2001-04-03, released 2001-09-28
The last revision prior to the SCOPe 2.03 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 3.1 Å
R-factor: 0.223
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: histone h3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: HISTONE H3
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61830
      • conflict (122)
    Domains in SCOPe 2.03: d1id3a_
  • Chain 'B':
    Compound: histone h4
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: HISTONE H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d1id3b_
  • Chain 'C':
    Compound: histone h2a.1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: HISTONE H2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d1id3c_
  • Chain 'D':
    Compound: histone h2b.2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: HISTONE H2B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d1id3d_
  • Chain 'E':
    Compound: histone h3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: HISTONE H3
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61830
      • conflict (122)
    Domains in SCOPe 2.03: d1id3e_
  • Chain 'F':
    Compound: histone h4
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: HISTONE H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d1id3f_
  • Chain 'G':
    Compound: histone h2a.1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: HISTONE H2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d1id3g_
  • Chain 'H':
    Compound: histone h2b.2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: HISTONE H2B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d1id3h_
  • Chain 'I':
    Compound: palindromic 146bp DNA fragment
    Species: Homo sapiens [TaxId:9606]
    Gene: ALPHA SAT DNA
  • Chain 'J':
    Compound: palindromic 146bp DNA fragment
    Species: Homo sapiens [TaxId:9606]
    Gene: ALPHA SAT DNA
  • Heterogens: MN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >1id3A (A:)
    artkqtarkstggkaprkqlaskaarksapstggvkkphrykpgtvalreirrfqkstel
    lirklpfqrlvreiaqdfktdlrfqssaigalqesveaylvslfedtnlaaihakrvtiq
    kkeiklarrlrgers
    

    Sequence, based on observed residues (ATOM records): (download)
    >1id3A (A:)
    phrykpgtvalreirrfqkstellirklpfqrlvreiaqdfktdlrfqssaigalqesve
    aylvslfedtnlaaihakrvtiqkkeiklarrlrger
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1id3B (B:)
    sgrgkggkglgkggakrhrkilrdniqgitkpairrlarrggvkrisgliyeevravlks
    flesvirdsvtytehakrktvtsldvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >1id3B (B:)
    dniqgitkpairrlarrggvkrisgliyeevravlksflesvirdsvtytehakrktvts
    ldvvyalkrqgrtlygfgg
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1id3C (C:)
    sggkggkagsaakasqsrsakagltfpvgrvhrllrrgnyaqrigsgapvyltavleyla
    aeilelagnaardnkktriiprhlqlairnddelnkllgnvtiaqggvlpnihqnllpkk
    sakatkasqel
    

    Sequence, based on observed residues (ATOM records): (download)
    >1id3C (C:)
    qsrsakagltfpvgrvhrllrrgnyaqrigsgapvyltavleylaaeilelagnaardnk
    ktriiprhlqlairnddelnkllgnvtiaqggvlpnihqnllpkksakat
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >1id3D (D:)
    ssaaekkpaskapaekkpaakktstsvdgkkrskvrketyssyiykvlkqthpdtgisqk
    smsilnsfvndiferiateasklaaynkkstisareiqtavrlilpgelakhavsegtra
    vtkyssstqa
    

    Sequence, based on observed residues (ATOM records): (download)
    >1id3D (D:)
    rketyssyiykvlkqthpdtgisqksmsilnsfvndiferiateasklaaynkkstisar
    eiqtavrlilpgelakhavsegtravtkyssst
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >1id3E (E:)
    artkqtarkstggkaprkqlaskaarksapstggvkkphrykpgtvalreirrfqkstel
    lirklpfqrlvreiaqdfktdlrfqssaigalqesveaylvslfedtnlaaihakrvtiq
    kkeiklarrlrgers
    

    Sequence, based on observed residues (ATOM records): (download)
    >1id3E (E:)
    phrykpgtvalreirrfqkstellirklpfqrlvreiaqdfktdlrfqssaigalqesve
    aylvslfedtnlaaihakrvtiqkkeiklarrlrger
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >1id3F (F:)
    sgrgkggkglgkggakrhrkilrdniqgitkpairrlarrggvkrisgliyeevravlks
    flesvirdsvtytehakrktvtsldvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >1id3F (F:)
    hrkilrdniqgitkpairrlarrggvkrisgliyeevravlksflesvirdsvtytehak
    rktvtsldvvyalkrqgrtlygfgg
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >1id3G (G:)
    sggkggkagsaakasqsrsakagltfpvgrvhrllrrgnyaqrigsgapvyltavleyla
    aeilelagnaardnkktriiprhlqlairnddelnkllgnvtiaqggvlpnihqnllpkk
    sakatkasqel
    

    Sequence, based on observed residues (ATOM records): (download)
    >1id3G (G:)
    kasqsrsakagltfpvgrvhrllrrgnyaqrigsgapvyltavleylaaeilelagnaar
    dnkktriiprhlqlairnddelnkllgnvtiaqggvlpnihqnllpkk
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >1id3H (H:)
    ssaaekkpaskapaekkpaakktstsvdgkkrskvrketyssyiykvlkqthpdtgisqk
    smsilnsfvndiferiateasklaaynkkstisareiqtavrlilpgelakhavsegtra
    vtkyssstqa
    

    Sequence, based on observed residues (ATOM records): (download)
    >1id3H (H:)
    vrketyssyiykvlkqthpdtgisqksmsilnsfvndiferiateasklaaynkkstisa
    reiqtavrlilpgelakhavsegtravtkyssstqa
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.