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 2.08 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):
Domains in SCOPe 2.08: d1id3a_ - Chain 'B':
Compound: histone h4
Species: Saccharomyces cerevisiae [TaxId:4932]
Gene: HISTONE H4
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: 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 2.08: 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 2.08: d1id3d_ - Chain 'E':
Compound: histone h3
Species: Saccharomyces cerevisiae [TaxId:4932]
Gene: HISTONE H3
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d1id3e_ - Chain 'F':
Compound: histone h4
Species: Saccharomyces cerevisiae [TaxId:4932]
Gene: HISTONE H4
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: 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 2.08: 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 2.08: 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.