General information
PDB ID 3GUT
Title CRYSTAL STRUCTURE OF A HIGHER-ORDER COMPLEX OF P50:RELA BOUND TO THE HIV-1 LTR
PDB header TRANSCRIPTION/DNA
Date 2009-03-30
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.59
Kind dna
Organism HOMO SAPIENS, HUMAN IMMUNODEFICIENCY VIRUS
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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:
pdb3gut.pdb ABCDEFGH XYIJ 0
Biounits:
3gut.pdb1.pdb ABCD XY 1
3gut.pdb2.pdb EFGH IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
RHD_DNA_bind Domain Q04206_21-186 7.9e-70 1 CL0073 A 21 186 XY  L-Bb L-Mj 
RHD_dimer Domain Q04206_195-291 9.3e-37 1 CL0159 A 195 291   
RHD_DNA_bind Domain P19838_44-242 8.3e-74 1 CL0073 B 342 540 XY  H-Bb H-Mj L-Bb L-Mj 
RHD_dimer Domain P19838_251-352 2.9e-40 1 CL0159 B 549 650 Y  L-Bb 
RHD_DNA_bind Domain Q04206_21-186 7.9e-70 1 CL0073 C 21 186 XY  L-Bb L-Mj 
RHD_dimer Domain Q04206_195-291 9.3e-37 1 CL0159 C 195 291 X  L-Bb 
RHD_DNA_bind Domain P19838_44-242 8.3e-74 1 CL0073 D 342 540 XY  H-Bb H-Mj L-Bb L-Mj 
RHD_dimer Domain P19838_251-352 2.9e-40 1 CL0159 D 549 650 Y  L-Bb 
RHD_DNA_bind Domain Q04206_21-186 7.9e-70 1 CL0073 E 21 186 IJ  L-Bb L-Mj 
RHD_dimer Domain Q04206_195-291 9.3e-37 1 CL0159 E 195 291   
RHD_DNA_bind Domain P19838_44-242 8.3e-74 1 CL0073 F 342 540 IJ  H-Bb H-Mj L-Bb L-Mj 
RHD_dimer Domain P19838_251-352 2.9e-40 1 CL0159 F 549 650 J  L-Bb 
RHD_DNA_bind Domain Q04206_21-186 7.9e-70 1 CL0073 G 21 186 IJ  L-Bb L-Mj 
RHD_dimer Domain Q04206_195-291 9.3e-37 1 CL0159 G 195 291 I  L-Bb 
RHD_DNA_bind Domain P19838_44-242 8.3e-74 1 CL0073 H 342 540 IJ  H-Bb H-Mj L-Bb L-Mj 
RHD_dimer Domain P19838_251-352 2.9e-40 1 CL0159 H 549 650 J  L-Bb 
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/C/E/G=20-291 C cytoplasm
A/C/E/G=20-291 C cytosol
A/C/E/G=20-291 C glutamatergic synapse
A/C/E/G=20-291 C host cell nucleus
A/C/E/G=20-291 C NF-kappaB p50/p65 complex
A/C/E/G=20-291 C nuclear chromatin
A/C/E/G=20-291 C nucleoplasm
A/C/E/G=20-291 C nucleus
A/C/E/G=20-291 C transcription regulator complex
A/C/E/G=20-291 F actinin binding
A/C/E/G=20-291 F activating transcription factor binding
A/C/E/G=20-291 F ankyrin repeat binding
A/C/E/G=20-291 F chromatin binding
A/C/E/G=20-291 F chromatin DNA binding
A/C/E/G=20-291 F DNA binding
A/C/E/G=20-291 F DNA-binding transcription activator activity, RNA polymerase II-specific
A/C/E/G=20-291 F DNA-binding transcription factor activity
A/C/E/G=20-291 F DNA-binding transcription factor activity, RNA polymerase II-specific
A/C/E/G=20-291 F DNA-binding transcription repressor activity, RNA polymerase II-specific
A/C/E/G=20-291 F enzyme binding
A/C/E/G=20-291 F histone deacetylase binding
A/C/E/G=20-291 F identical protein binding
A/C/E/G=20-291 F NF-kappaB binding
A/C/E/G=20-291 F peptide binding
A/C/E/G=20-291 F phosphate ion binding
A/C/E/G=20-291 F protein homodimerization activity
A/C/E/G=20-291 F protein kinase binding
A/C/E/G=20-291 F protein N-terminus binding
A/C/E/G=20-291 F protein-containing complex binding
A/C/E/G=20-291 F repressing transcription factor binding
A/C/E/G=20-291 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
A/C/E/G=20-291 F RNA polymerase II core promoter sequence-specific DNA binding
A/C/E/G=20-291 F RNA polymerase II transcription coactivator binding
A/C/E/G=20-291 F RNA polymerase II transcription regulatory region sequence-specific DNA binding
A/C/E/G=20-291 F transcription factor binding
A/C/E/G=20-291 F transcription regulatory region sequence-specific DNA binding
A/C/E/G=20-291 F ubiquitin protein ligase binding
A/C/E/G=20-291 P acetaldehyde metabolic process
A/C/E/G=20-291 P aging
A/C/E/G=20-291 P animal organ morphogenesis
A/C/E/G=20-291 P cellular defense response
A/C/E/G=20-291 P cellular response to angiotensin
A/C/E/G=20-291 P cellular response to hepatocyte growth factor stimulus
A/C/E/G=20-291 P cellular response to hydrogen peroxide
A/C/E/G=20-291 P cellular response to interleukin-1
A/C/E/G=20-291 P cellular response to interleukin-6
A/C/E/G=20-291 P cellular response to lipopolysaccharide
A/C/E/G=20-291 P cellular response to lipoteichoic acid
A/C/E/G=20-291 P cellular response to nicotine
A/C/E/G=20-291 P cellular response to peptidoglycan
A/C/E/G=20-291 P cellular response to tumor necrosis factor
A/C/E/G=20-291 P cellular response to vascular endothelial growth factor stimulus
A/C/E/G=20-291 P chromatin organization
A/C/E/G=20-291 P cytokine-mediated signaling pathway
A/C/E/G=20-291 P defense response to virus
A/C/E/G=20-291 P Fc-epsilon receptor signaling pathway
A/C/E/G=20-291 P hair follicle development
A/C/E/G=20-291 P I-kappaB kinase/NF-kappaB signaling
A/C/E/G=20-291 P inflammatory response
A/C/E/G=20-291 P innate immune response
A/C/E/G=20-291 P interleukin-1-mediated signaling pathway
A/C/E/G=20-291 P liver development
A/C/E/G=20-291 P membrane protein intracellular domain proteolysis
A/C/E/G=20-291 P negative regulation of apoptotic process
A/C/E/G=20-291 P negative regulation of extrinsic apoptotic signaling pathway
A/C/E/G=20-291 P negative regulation of insulin receptor signaling pathway
A/C/E/G=20-291 P negative regulation of NIK/NF-kappaB signaling
A/C/E/G=20-291 P negative regulation of pri-miRNA transcription by RNA polymerase II
A/C/E/G=20-291 P negative regulation of protein catabolic process
A/C/E/G=20-291 P negative regulation of protein sumoylation
A/C/E/G=20-291 P negative regulation of transcription by RNA polymerase II
A/C/E/G=20-291 P negative regulation of transcription, DNA-templated
A/C/E/G=20-291 P NIK/NF-kappaB signaling
A/C/E/G=20-291 P nucleotide-binding oligomerization domain containing 2 signaling pathway
A/C/E/G=20-291 P positive regulation of amyloid-beta formation
A/C/E/G=20-291 P positive regulation of cell population proliferation
A/C/E/G=20-291 P positive regulation of chondrocyte differentiation
A/C/E/G=20-291 P positive regulation of I-kappaB kinase/NF-kappaB signaling
A/C/E/G=20-291 P positive regulation of interleukin-12 production
A/C/E/G=20-291 P positive regulation of interleukin-8 production
A/C/E/G=20-291 P positive regulation of leukocyte adhesion to vascular endothelial cell
A/C/E/G=20-291 P positive regulation of miRNA metabolic process
A/C/E/G=20-291 P positive regulation of NF-kappaB transcription factor activity
A/C/E/G=20-291 P positive regulation of NIK/NF-kappaB signaling
A/C/E/G=20-291 P positive regulation of pri-miRNA transcription by RNA polymerase II
A/C/E/G=20-291 P positive regulation of Schwann cell differentiation
A/C/E/G=20-291 P positive regulation of T cell receptor signaling pathway
A/C/E/G=20-291 P positive regulation of transcription by RNA polymerase II
A/C/E/G=20-291 P positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
A/C/E/G=20-291 P positive regulation of transcription, DNA-templated
A/C/E/G=20-291 P positive regulation of type I interferon production
A/C/E/G=20-291 P postsynapse to nucleus signaling pathway
A/C/E/G=20-291 P regulation of DNA-templated transcription in response to stress
A/C/E/G=20-291 P regulation of inflammatory response
A/C/E/G=20-291 P regulation of NIK/NF-kappaB signaling
A/C/E/G=20-291 P regulation of transcription, DNA-templated
A/C/E/G=20-291 P response to amino acid
A/C/E/G=20-291 P response to cAMP
A/C/E/G=20-291 P response to cobalamin
A/C/E/G=20-291 P response to cytokine
A/C/E/G=20-291 P response to drug
A/C/E/G=20-291 P response to insulin
A/C/E/G=20-291 P response to interleukin-1
A/C/E/G=20-291 P response to morphine
A/C/E/G=20-291 P response to muramyl dipeptide
A/C/E/G=20-291 P response to muscle stretch
A/C/E/G=20-291 P response to organic substance
A/C/E/G=20-291 P response to progesterone
A/C/E/G=20-291 P response to UV-B
A/C/E/G=20-291 P stimulatory C-type lectin receptor signaling pathway
A/C/E/G=20-291 P T cell receptor signaling pathway
A/C/E/G=20-291 P transcription, DNA-templated
A/C/E/G=20-291 P tumor necrosis factor-mediated signaling pathway
A/C/E/G=20-291 P viral process
B/D/F/H=41-352 C cytoplasm
B/D/F/H=41-352 C cytosol
B/D/F/H=41-352 C extracellular region
B/D/F/H=41-352 C host cell nucleus
B/D/F/H=41-352 C I-kappaB/NF-kappaB complex
B/D/F/H=41-352 C mitochondrion
B/D/F/H=41-352 C nuclear chromatin
B/D/F/H=41-352 C nucleoplasm
B/D/F/H=41-352 C nucleus
B/D/F/H=41-352 C secretory granule lumen
B/D/F/H=41-352 C specific granule lumen
B/D/F/H=41-352 F actinin binding
B/D/F/H=41-352 F chromatin binding
B/D/F/H=41-352 F DNA-binding transcription activator activity, RNA polymerase II-specific
B/D/F/H=41-352 F DNA-binding transcription factor activity
B/D/F/H=41-352 F DNA-binding transcription factor activity, RNA polymerase II-specific
B/D/F/H=41-352 F DNA-binding transcription repressor activity, RNA polymerase II-specific
B/D/F/H=41-352 F enzyme binding
B/D/F/H=41-352 F identical protein binding
B/D/F/H=41-352 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
B/D/F/H=41-352 F RNA polymerase II transcription coactivator binding
B/D/F/H=41-352 F RNA polymerase II transcription regulatory region sequence-specific DNA binding
B/D/F/H=41-352 F transcription factor binding
B/D/F/H=41-352 F transcription regulatory region sequence-specific DNA binding
B/D/F/H=41-352 P apoptotic process
B/D/F/H=41-352 P cellular response to angiotensin
B/D/F/H=41-352 P cellular response to dsRNA
B/D/F/H=41-352 P cellular response to interleukin-1
B/D/F/H=41-352 P cellular response to interleukin-6
B/D/F/H=41-352 P cellular response to lipopolysaccharide
B/D/F/H=41-352 P cellular response to mechanical stimulus
B/D/F/H=41-352 P cellular response to nicotine
B/D/F/H=41-352 P cellular response to tumor necrosis factor
B/D/F/H=41-352 P Fc-epsilon receptor signaling pathway
B/D/F/H=41-352 P inflammatory response
B/D/F/H=41-352 P interleukin-1-mediated signaling pathway
B/D/F/H=41-352 P membrane protein intracellular domain proteolysis
B/D/F/H=41-352 P negative regulation of apoptotic process
B/D/F/H=41-352 P negative regulation of calcidiol 1-monooxygenase activity
B/D/F/H=41-352 P negative regulation of cellular protein metabolic process
B/D/F/H=41-352 P negative regulation of cholesterol transport
B/D/F/H=41-352 P negative regulation of gene expression
B/D/F/H=41-352 P negative regulation of inflammatory response
B/D/F/H=41-352 P negative regulation of interleukin-12 production
B/D/F/H=41-352 P negative regulation of transcription by RNA polymerase II
B/D/F/H=41-352 P negative regulation of vitamin D biosynthetic process
B/D/F/H=41-352 P neutrophil degranulation
B/D/F/H=41-352 P positive regulation of canonical Wnt signaling pathway
B/D/F/H=41-352 P positive regulation of hyaluronan biosynthetic process
B/D/F/H=41-352 P positive regulation of lipid storage
B/D/F/H=41-352 P positive regulation of macrophage derived foam cell differentiation
B/D/F/H=41-352 P positive regulation of miRNA metabolic process
B/D/F/H=41-352 P positive regulation of NF-kappaB transcription factor activity
B/D/F/H=41-352 P positive regulation of transcription by RNA polymerase II
B/D/F/H=41-352 P positive regulation of transcription, DNA-templated
B/D/F/H=41-352 P positive regulation of type I interferon production
B/D/F/H=41-352 P response to muscle stretch
B/D/F/H=41-352 P stimulatory C-type lectin receptor signaling pathway
B/D/F/H=41-352 P stress-activated MAPK cascade
B/D/F/H=41-352 P T cell receptor signaling pathway
B/D/F/H=41-352 P transcription by RNA polymerase II
Sequences
Download file with secondary structure created by Stride  
3gut.pdb1.pdb:   [ download sequences in FASTA format ]
X (dna): 
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Y (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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3gut.pdb2.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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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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