General information
PDB ID 6O1D
Title CRYO-EM STRUCTURE OF THE CENTROMERIC NUCLEOSOME WITH NATIVE ALPHA SATELLITE DNA
PDB header NUCLEAR PROTEIN
Date 2019-02-19
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.4
Kind dna
Organism HOMO SAPIENS
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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:
pdb6o1d.pdb ABCDEFGH IJ 0
Biounits:
6o1d.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 P49450_42-133 3.1e-34 1 CL0012 A 42 133 IJ  H-Bb H-Mj S-Bb L-Bb L-Mn 
CENP-T_C Domain P62805_26-99 4.6e-08 1 CL0012 B 26 98 IJ  H-Bb S-Bb L-Bb 
Histone Domain P04908_10-91 2e-16 1 CL0012 C 10 90 IJ  H-Bb S-Bb L-Bb 
Histone Domain P06899_33-102 5.5e-22 1 CL0012 D 31 101 IJ  H-Bb H-Mj S-Bb L-Bb 
Histone Domain P49450_42-133 3.1e-34 1 CL0012 E 42 133 IJ  H-Bb H-Mj S-Bb L-Bb 
CENP-T_C Domain P62805_26-99 4.6e-08 1 CL0012 F 26 98 IJ  H-Bb S-Bb L-Bb 
Histone Domain P04908_10-91 1.4e-16 1 CL0012 G 9 90 IJ  H-Bb S-Bb L-Bb L-Mn 
Histone Domain P06899_33-102 5.5e-22 1 CL0012 H 31 101 IJ  H-Bb H-Mj S-Bb L-Bb 
Histone_H2A_C Family P04908_92-119 2.2e-15 1 No_clan C 91 116   
Histone_H2A_C Family P04908_92-119 2.2e-15 1 No_clan G 91 116   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E=1-140 C chromosome, centromeric region
A/E=1-140 C condensed chromosome inner kinetochore
A/E=1-140 C condensed nuclear chromosome kinetochore
A/E=1-140 C condensed nuclear chromosome, centromeric region
A/E=1-140 C cytosol
A/E=1-140 C nuclear nucleosome
A/E=1-140 C nuclear pericentric heterochromatin
A/E=1-140 C nucleoplasm
A/E=1-140 C nucleus
A/E=1-140 F chromatin binding
A/E=1-140 F DNA binding
A/E=1-140 F protein heterodimerization activity
A/E=1-140 P CENP-A containing nucleosome assembly
A/E=1-140 P establishment of mitotic spindle orientation
A/E=1-140 P kinetochore assembly
A/E=1-140 P mitotic cytokinesis
A/E=1-140 P protein localization to chromosome, centromeric region
A/E=1-140 P viral process
B/F=1-103 C extracellular exosome
B/F=1-103 C extracellular region
B/F=1-103 C host cell nucleus
B/F=1-103 C membrane
B/F=1-103 C nuclear chromosome
B/F=1-103 C nuclear chromosome, telomeric region
B/F=1-103 C nuclear nucleosome
B/F=1-103 C nucleoplasm
B/F=1-103 C nucleosome
B/F=1-103 C nucleus
B/F=1-103 C protein-containing complex
B/F=1-103 F DNA binding
B/F=1-103 F protein domain specific binding
B/F=1-103 F protein heterodimerization activity
B/F=1-103 F RNA binding
B/F=1-103 P cellular protein metabolic process
B/F=1-103 P CENP-A containing nucleosome assembly
B/F=1-103 P DNA replication-dependent nucleosome assembly
B/F=1-103 P DNA replication-independent nucleosome assembly
B/F=1-103 P DNA-templated transcription, initiation
B/F=1-103 P double-strand break repair via nonhomologous end joining
B/F=1-103 P negative regulation of gene expression, epigenetic
B/F=1-103 P negative regulation of megakaryocyte differentiation
B/F=1-103 P nucleosome assembly
B/F=1-103 P rDNA heterochromatin assembly
B/F=1-103 P regulation of gene silencing by miRNA
B/F=1-103 P regulation of megakaryocyte differentiation
B/F=1-103 P telomere capping
B/F=1-103 P telomere organization
C/G=1-130 C extracellular exosome
C/G=1-130 C nuclear chromatin
C/G=1-130 C nucleosome
C/G=1-130 C nucleus
C/G=1-130 F DNA binding
C/G=1-130 F protein heterodimerization activity
C/G=1-130 P chromatin organization
C/G=1-130 P chromatin silencing
C/G=1-130 P negative regulation of cell population proliferation
D/H=1-126 C cytosol
D/H=1-126 C extracellular space
D/H=1-126 C nucleoplasm
D/H=1-126 C nucleosome
D/H=1-126 C nucleus
D/H=1-126 F DNA binding
D/H=1-126 F lipopolysaccharide binding
D/H=1-126 F protein heterodimerization activity
D/H=1-126 P antibacterial humoral response
D/H=1-126 P antimicrobial humoral immune response mediated by antimicrobial peptide
D/H=1-126 P defense response to Gram-negative bacterium
D/H=1-126 P defense response to Gram-positive bacterium
D/H=1-126 P innate immune response in mucosa
D/H=1-126 P killing of cells of other organism
D/H=1-126 P negative regulation of tumor necrosis factor-mediated signaling pathway
D/H=1-126 P nucleosome assembly
D/H=1-126 P protein ubiquitination
Sequences
Download file with secondary structure created by Stride  
6o1d.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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