General information
PDB ID 6RNY
Title PFV INTASOME - NUCLEOSOME STRAND TRANSFER COMPLEX
PDB header DNA BINDING PROTEIN
Date 2019-05-09
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.9
Kind dna
Organism HOMO SAPIENS, HUMAN SPUMARETROVIRUS, PYROBACULUM FILAMENTOUS VIRUS 1
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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:
pdb6rny.pdb ABCDEFGHKLOP IUTJQM 0
Biounits:
6rny.pdb1.pdb ABCDEFGHKLOP IUTJQM 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain P84243_39-132 3.4e-45 1 CL0012 A 39 131 IU   
CENP-T_C Domain P62805_19-99 4.9e-08 1 CL0012 B 25 98 IU   
Histone Domain P0C0S8_10-91 2.9e-16 1 CL0012 C 9 90 JT   
Histone Domain P62807_29-102 2e-21 1 CL0012 D 29 98 JT   
Histone Domain P84243_39-132 3.4e-45 1 CL0012 E 39 131 IJU   
CENP-T_C Domain P62805_19-99 4.9e-08 1 CL0012 F 25 98 I   
Histone Domain P0C0S8_10-91 2.9e-16 1 CL0012 G 9 90 IU   
Histone Domain P62807_29-102 2e-21 1 CL0012 H 29 98 U   
SH3_11 Domain P14350_1064-1125 2.9e-45 1 CL0010 K 313 375 IMQ  L-Bb 
Integrase_H2C2 Domain P14350_800-856 2.9e-15 1 CL0361 K 49 105 Q   
rve Domain P14350_869-965 3.8e-13 1 CL0219 K 118 214 IUJ   
rve Domain P14350_869-960 2e-11 1 CL0219 L 121 225   
SH3_11 Domain P14350_1064-1125 2.9e-45 1 CL0010 O 313 375 JMQT  L-Bb L-Mn 
Integrase_H2C2 Domain P14350_800-856 2.9e-15 1 CL0361 O 49 105 JM  H-Bb 
rve Domain P14350_869-965 3.8e-13 1 CL0219 O 118 214 IJT   
rve Domain P14350_869-960 1.5e-11 1 CL0219 P 118 220   
Histone_H2A_C Family P0C0S8_92-122 3.5e-17 1 No_clan C 91 118   
Histone_H2A_C Family P0C0S8_92-122 3.5e-17 1 No_clan G 91 118   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E=1-136 C Barr body
A/E=1-136 C extracellular exosome
A/E=1-136 C extracellular region
A/E=1-136 C nuclear chromosome
A/E=1-136 C nuclear chromosome, telomeric region
A/E=1-136 C nuclear nucleosome
A/E=1-136 C nucleoplasm
A/E=1-136 C nucleosome
A/E=1-136 C nucleus
A/E=1-136 C protein-containing complex
A/E=1-136 F nucleosomal DNA binding
A/E=1-136 F protein heterodimerization activity
A/E=1-136 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
A/E=1-136 F RNA polymerase II core promoter sequence-specific DNA binding
A/E=1-136 P blood coagulation
A/E=1-136 P brain development
A/E=1-136 P cell population proliferation
A/E=1-136 P cellular protein metabolic process
A/E=1-136 P DNA replication-independent nucleosome assembly
A/E=1-136 P embryo implantation
A/E=1-136 P male gonad development
A/E=1-136 P multicellular organism growth
A/E=1-136 P muscle cell differentiation
A/E=1-136 P negative regulation of chromosome condensation
A/E=1-136 P negative regulation of gene expression, epigenetic
A/E=1-136 P nucleosome assembly
A/E=1-136 P nucleus organization
A/E=1-136 P oogenesis
A/E=1-136 P osteoblast differentiation
A/E=1-136 P pericentric heterochromatin assembly
A/E=1-136 P positive regulation of cell growth
A/E=1-136 P rDNA heterochromatin assembly
A/E=1-136 P regulation of centromere complex assembly
A/E=1-136 P regulation of gene silencing by miRNA
A/E=1-136 P regulation of megakaryocyte differentiation
A/E=1-136 P response to hormone
A/E=1-136 P single fertilization
A/E=1-136 P spermatid development
A/E=1-136 P subtelomeric heterochromatin assembly
A/E=1-136 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 enzyme binding
C/G=1-130 F protein heterodimerization activity
C/G=1-130 P chromatin organization
C/G=1-130 P chromatin silencing
D/H=1-126 C cytosol
D/H=1-126 C extracellular exosome
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 identical protein 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-positive bacterium
D/H=1-126 P innate immune response in mucosa
D/H=1-126 P nucleosome assembly
D/H=1-126 P protein ubiquitination
K/L/O/P=754-1143 C host cell cytoplasm
K/L/O/P=754-1143 C host cell nucleus
K/L/O/P=754-1143 C virion
K/L/O/P=754-1143 F aspartic-type endopeptidase activity
K/L/O/P=754-1143 F DNA-directed DNA polymerase activity
K/L/O/P=754-1143 F identical protein binding
K/L/O/P=754-1143 F metal ion binding
K/L/O/P=754-1143 F RNA binding
K/L/O/P=754-1143 F RNA-directed DNA polymerase activity
K/L/O/P=754-1143 F RNA-DNA hybrid ribonuclease activity
K/L/O/P=754-1143 P DNA integration
K/L/O/P=754-1143 P DNA recombination
K/L/O/P=754-1143 P establishment of integrated proviral latency
K/L/O/P=754-1143 P viral entry into host cell
K/L/O/P=754-1143 P viral genome integration into host DNA
K/L/O/P=754-1143 P viral penetration into host nucleus
Sequences
Download file with secondary structure created by Stride  
6rny.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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M (dna): 
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Q (dna): 
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T (dna): 
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U (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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O (protein): 
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P (protein): 
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