General information
PDB ID 1ID3
Title CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS
PDB header STRUCTURAL PROTEIN/DNA
Date 2001-04-03
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.1
Kind dna
Organism HOMO SAPIENS, SACCHAROMYCES CEREVISIAE
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb1id3.pdb ABCDEFGH IJ 0
Biounits:
1id3.pdb1.pdb ABCDEFGH IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain P61830_39-132 1.9e-40 1 CL0012 A 38 131 IJ  H-Bb H-Mj S-Bb L-Bb L-Mn 
CENP-T_C Domain P02309_25-99 6.3e-09 1 CL0012 B 26 98 IJ  H-Bb S-Bb L-Bb 
Histone Domain P04911_14-92 1e-15 1 CL0012 C 16 91 IJ  H-Bb S-Bb L-Bb 
Histone Domain P02294_36-105 2.9e-17 1 CL0012 D 36 104 I  S-Bb L-Bb L-Mn 
Histone Domain P61830_39-132 1.9e-40 1 CL0012 E 38 131 IJ  H-Bb H-Mj S-Bb L-Bb L-Mn 
CENP-T_C Domain P02309_19-99 7.2e-09 1 CL0012 F 23 98 IJ  H-Bb H-Mj S-Bb L-Bb 
Histone Domain P04911_14-92 1.2e-16 1 CL0012 G 13 91 IJ  H-Bb S-Bb L-Bb 
Histone Domain P02294_36-105 2.3e-17 1 CL0012 H 35 104 IJ  H-Bb S-Bb L-Bb 
Histone_H2A_C Family P04911_93-126 1.5e-20 1 No_clan C 92 125   
Histone_H2A_C Family P04911_93-121 1.2e-18 1 No_clan G 92 120   
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: All alpha proteins
  Fold: Histone-fold
    Superfamily: Histone-fold
      Family: Nucleosome core histones
Histone H2B D N/A N/A I  S-Bb L-Bb L-Mn 
Class: All alpha proteins
  Fold: Histone-fold
    Superfamily: Histone-fold
      Family: Nucleosome core histones
Histone H2B H N/A N/A IJ  H-Bb S-Bb L-Bb 
Class: All alpha proteins
  Fold: Histone-fold
    Superfamily: Histone-fold
      Family: Nucleosome core histones
Histone H3 A N/A N/A IJ  H-Bb H-Mj S-Bb L-Bb L-Mn 
Class: All alpha proteins
  Fold: Histone-fold
    Superfamily: Histone-fold
      Family: Nucleosome core histones
Histone H3 E N/A N/A IJ  H-Bb H-Mj S-Bb L-Bb L-Mn 
Class: All alpha proteins
  Fold: Histone-fold
    Superfamily: Histone-fold
      Family: Nucleosome core histones
Histone H4 B N/A N/A IJ  H-Bb S-Bb L-Bb 
Class: All alpha proteins
  Fold: Histone-fold
    Superfamily: Histone-fold
      Family: Nucleosome core histones
Histone H4 F N/A N/A IJ  H-Bb H-Mj S-Bb L-Bb 
Class: All alpha proteins
  Fold: Histone-fold
    Superfamily: Histone-fold
      Family: Nucleosome core histones
Histone H2A C N/A N/A IJ  H-Bb S-Bb L-Bb 
Class: All alpha proteins
  Fold: Histone-fold
    Superfamily: Histone-fold
      Family: Nucleosome core histones
Histone H2A G N/A N/A IJ  H-Bb S-Bb L-Bb 
GO terms
Protein chains: GO type: GO description:
A/E=2-136 C CENP-A containing nucleosome
A/E=2-136 C nuclear nucleosome
A/E=2-136 C nucleus
A/E=2-136 C replication fork protection complex
A/E=2-136 F DNA binding
A/E=2-136 F protein heterodimerization activity
A/E=2-136 P chromatin assembly or disassembly
A/E=2-136 P global genome nucleotide-excision repair
A/E=2-136 P rRNA transcription
A/E=2-136 P sexual sporulation resulting in formation of a cellular spore
B/F=2-103 C host cell nucleus
B/F=2-103 C nuclear nucleosome
B/F=2-103 C replication fork protection complex
B/F=2-103 F DNA binding
B/F=2-103 F protein heterodimerization activity
B/F=2-103 P chromatin assembly or disassembly
B/F=2-103 P histone H3-K79 methylation
B/F=2-103 P nucleosome assembly
B/F=2-103 P sexual sporulation resulting in formation of a cellular spore
B/F=2-103 P transfer RNA gene-mediated silencing
C/G=2-132 C nuclear chromatin
C/G=2-132 C nuclear nucleosome
C/G=2-132 C replication fork protection complex
C/G=2-132 F DNA binding
C/G=2-132 F protein heterodimerization activity
C/G=2-132 P chromatin assembly or disassembly
C/G=2-132 P chromatin organization
C/G=2-132 P chromatin silencing
C/G=2-132 P DNA repair
C/G=2-132 P negative regulation of transcription by RNA polymerase II
C/G=2-132 P transfer RNA gene-mediated silencing
D/H=2-131 C nuclear nucleosome
D/H=2-131 C replication fork protection complex
D/H=2-131 F DNA binding
D/H=2-131 F protein heterodimerization activity
D/H=2-131 P chromatin assembly or disassembly
D/H=2-131 P nucleosome assembly
Sequences
Download file with secondary structure created by Stride  
1id3.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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