General information
PDB ID 6YOV
Title OCT4-SOX2-BOUND NUCLEOSOME - SHL+6
PDB header TRANSCRIPTION
Date 2020-04-15
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.42
Kind dna
Organism HOMO SAPIENS, SYNTHETIC CONSTRUCT, AEQUOREA VICTORIA, 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:
pdb6yov.pdb ABCDEFGHKL IJ 0
Biounits:
6yov.pdb1.pdb ABCDEFGHKL IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain P68431_39-132 2.6e-46 1 CL0012 A 40 132 IJ  H-Bb H-Mj S-Bb L-Bb 
CENP-T_C Domain P62805_26-99 4.7e-08 1 CL0012 B 26 99 IJ  H-Bb S-Bb L-Bb 
Histone Domain P04908_10-91 1.2e-16 1 CL0012 C 9 91 IJ  H-Bb S-Bb L-Bb 
Histone Domain P06899_33-102 9.4e-22 1 CL0012 D 33 102 I  H-Bb S-Bb L-Bb 
Histone Domain P68431_39-132 2.6e-46 1 CL0012 E 40 132 IJ  H-Bb H-Mj S-Bb L-Bb 
CENP-T_C Domain P62805_26-99 4.4e-08 1 CL0012 F 26 99 IJ  H-Bb S-Bb L-Bb 
Histone Domain P04908_10-91 1.2e-16 1 CL0012 G 9 91 IJ  H-Bb S-Bb 
Histone Domain P06899_33-102 1.5e-21 1 CL0012 H 34 102 J  L-Bb 
Pou Domain Q01860_141-210 2.5e-35 1 CL0123 K 141 208   
HMG_box Domain P48431_41-109 4.6e-29 1 CL0114 L 41 109 IJ  H-Bb H-Mj H-Mn L-Bb L-Mn 
Histone_H2A_C Family P04908_92-119 2.5e-16 1 No_clan C 92 118   
Histone_H2A_C Family P04908_92-119 2.5e-16 1 No_clan G 92 118   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A=1-136, E=1-134 C extracellular exosome
A=1-136, E=1-134 C extracellular region
A=1-136, E=1-134 C membrane
A=1-136, E=1-134 C nuclear chromosome
A=1-136, E=1-134 C nuclear nucleosome
A=1-136, E=1-134 C nucleoplasm
A=1-136, E=1-134 C nucleosome
A=1-136, E=1-134 C nucleus
A=1-136, E=1-134 C protein-containing complex
A=1-136, E=1-134 F cadherin binding
A=1-136, E=1-134 F DNA binding
A=1-136, E=1-134 F protein heterodimerization activity
A=1-136, E=1-134 P blood coagulation
A=1-136, E=1-134 P cellular protein metabolic process
A=1-136, E=1-134 P chromatin organization
A=1-136, E=1-134 P DNA replication-dependent nucleosome assembly
A=1-136, E=1-134 P interleukin-7-mediated signaling pathway
A=1-136, E=1-134 P negative regulation of gene expression, epigenetic
A=1-136, E=1-134 P nucleosome assembly
A=1-136, E=1-134 P rDNA heterochromatin assembly
A=1-136, E=1-134 P regulation of gene silencing
A=1-136, E=1-134 P regulation of gene silencing by miRNA
A=1-136, E=1-134 P regulation of megakaryocyte differentiation
A=1-136, E=1-134 P telomere organization
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=1-125 C cytosol
D/H=1-125 C extracellular space
D/H=1-125 C nucleoplasm
D/H=1-125 C nucleosome
D/H=1-125 C nucleus
D/H=1-125 F DNA binding
D/H=1-125 F lipopolysaccharide binding
D/H=1-125 F protein heterodimerization activity
D/H=1-125 P antibacterial humoral response
D/H=1-125 P antimicrobial humoral immune response mediated by antimicrobial peptide
D/H=1-125 P defense response to Gram-negative bacterium
D/H=1-125 P defense response to Gram-positive bacterium
D/H=1-125 P innate immune response in mucosa
D/H=1-125 P killing of cells of other organism
D/H=1-125 P negative regulation of tumor necrosis factor-mediated signaling pathway
D/H=1-125 P nucleosome assembly
D/H=1-125 P protein ubiquitination
K=1-360 C cytoplasm
K=1-360 C cytosol
K=1-360 C mitochondrion
K=1-360 C nucleoplasm
K=1-360 C nucleus
K=1-360 C transcription regulator complex
K=1-360 F DNA binding
K=1-360 F DNA-binding transcription activator activity, RNA polymerase II-specific
K=1-360 F DNA-binding transcription factor activity
K=1-360 F DNA-binding transcription factor activity, RNA polymerase II-specific
K=1-360 F DNA-binding transcription repressor activity, RNA polymerase II-specific
K=1-360 F miRNA binding
K=1-360 F RNA binding
K=1-360 F sequence-specific DNA binding
K=1-360 F sequence-specific double-stranded DNA binding
K=1-360 F transcription factor binding
K=1-360 F transcription regulatory region sequence-specific DNA binding
K=1-360 F ubiquitin protein ligase binding
K=1-360 P anatomical structure morphogenesis
K=1-360 P blastocyst development
K=1-360 P BMP signaling pathway involved in heart induction
K=1-360 P cardiac cell fate determination
K=1-360 P cell differentiation
K=1-360 P cell fate commitment involved in formation of primary germ layer
K=1-360 P endodermal cell fate specification
K=1-360 P negative regulation of gene silencing by miRNA
K=1-360 P negative regulation of pri-miRNA transcription by RNA polymerase II
K=1-360 P negative regulation of transcription by RNA polymerase II
K=1-360 P positive regulation of canonical Wnt signaling pathway
K=1-360 P positive regulation of SMAD protein signal transduction
K=1-360 P positive regulation of transcription by RNA polymerase II
K=1-360 P regulation of asymmetric cell division
K=1-360 P regulation of DNA methylation-dependent heterochromatin assembly
K=1-360 P regulation of gene expression
K=1-360 P regulation of heart induction by regulation of canonical Wnt signaling pathway
K=1-360 P regulation of transcription by RNA polymerase II
K=1-360 P regulation of transcription, DNA-templated
K=1-360 P response to wounding
K=1-360 P somatic stem cell population maintenance
K=2-238 P bioluminescence
K=2-238 P generation of precursor metabolites and energy
K=2-238 P protein-chromophore linkage
L=37-118 C cytoplasm
L=37-118 C cytosol
L=37-118 C nuclear chromatin
L=37-118 C nucleoplasm
L=37-118 C nucleus
L=37-118 C transcription regulator complex
L=37-118 F DNA binding
L=37-118 F DNA-binding transcription activator activity, RNA polymerase II-specific
L=37-118 F DNA-binding transcription factor activity
L=37-118 F DNA-binding transcription factor activity, RNA polymerase II-specific
L=37-118 F miRNA binding
L=37-118 F sequence-specific DNA binding
L=37-118 F transcription regulatory region sequence-specific DNA binding
L=37-118 P adenohypophysis development
L=37-118 P anatomical structure morphogenesis
L=37-118 P cell cycle arrest
L=37-118 P cell differentiation
L=37-118 P cell fate commitment
L=37-118 P chromatin organization
L=37-118 P cytokine-mediated signaling pathway
L=37-118 P endodermal cell fate specification
L=37-118 P eye development
L=37-118 P forebrain development
L=37-118 P glial cell fate commitment
L=37-118 P inner ear development
L=37-118 P negative regulation of canonical Wnt signaling pathway
L=37-118 P negative regulation of epithelial cell proliferation
L=37-118 P negative regulation of neuron differentiation
L=37-118 P negative regulation of transcription by RNA polymerase II
L=37-118 P neuronal stem cell population maintenance
L=37-118 P osteoblast differentiation
L=37-118 P pituitary gland development
L=37-118 P positive regulation of cell differentiation
L=37-118 P positive regulation of cell-cell adhesion
L=37-118 P positive regulation of MAPK cascade
L=37-118 P positive regulation of transcription by RNA polymerase II
L=37-118 P positive regulation of transcription, DNA-templated
L=37-118 P regulation of cysteine-type endopeptidase activity involved in apoptotic process
L=37-118 P regulation of gene expression
L=37-118 P regulation of transcription, DNA-templated
L=37-118 P response to growth factor
L=37-118 P response to wounding
L=37-118 P somatic stem cell population maintenance
L=37-118 P tissue regeneration
Sequences
Download file with secondary structure created by Stride  
6yov.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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K (protein): 
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L (protein): 
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