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- PDB-2o61: Crystal Structure of NFkB, IRF7, IRF3 bound to the interferon-b e... -

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Basic information

Entry
Database: PDB / ID: 2o61
TitleCrystal Structure of NFkB, IRF7, IRF3 bound to the interferon-b enhancer
Components
  • 34-MER
  • 36-MER
  • Nuclear factor NF-kappa-B p105 subunit
  • Transcription factor p65/Interferon regulatory factor 7/Interferon regulatory factor 3 fusion protein
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


establishment of viral latency / interferon-alpha production / interferon-beta production / regulation of MyD88-independent toll-like receptor signaling pathway / regulation of monocyte differentiation / regulation of MyD88-dependent toll-like receptor signaling pathway / negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport ...establishment of viral latency / interferon-alpha production / interferon-beta production / regulation of MyD88-independent toll-like receptor signaling pathway / regulation of monocyte differentiation / regulation of MyD88-dependent toll-like receptor signaling pathway / negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / regulation of adaptive immune response / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / positive regulation of hyaluronan biosynthetic process / negative regulation of macrophage apoptotic process / antibacterial innate immune response / macrophage apoptotic process / mammary gland involution / acetaldehyde metabolic process / programmed necrotic cell death / cellular response to interleukin-17 / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / chromatin => GO:0000785 / IkBA variant leads to EDA-ID / positive regulation of macrophage derived foam cell differentiation / positive regulation of Schwann cell differentiation / regulation of type I interferon production / positive regulation of lipid storage / TRIF-dependent toll-like receptor signaling pathway / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / negative regulation of interleukin-12 production / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / SUMOylation of immune response proteins / negative regulation of protein sumoylation / cellular response to dsRNA / nucleotide-binding oligomerization domain containing 2 signaling pathway / postsynapse to nucleus signaling pathway / defense response to tumor cell / Interleukin-1 processing / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / cellular response to interleukin-6 / positive regulation of type I interferon-mediated signaling pathway / actinin binding / negative regulation of protein metabolic process / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / response to UV-B / mRNA transcription / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / DNA-binding transcription activator activity / immune system process / positive regulation of amyloid-beta formation / cellular response to exogenous dsRNA / positive regulation of T cell receptor signaling pathway / type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / response to cobalamin / phosphate ion binding / non-canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / cellular response to lipoteichoic acid / response to muramyl dipeptide / The NLRP3 inflammasome / immunoglobulin mediated immune response / general transcription initiation factor binding / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of type I interferon production / positive regulation of vascular endothelial growth factor production / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / regulation of immune response / canonical NF-kappaB signal transduction / response to amino acid / cellular response to interleukin-1 / cellular defense response / Purinergic signaling in leishmaniasis infection / type II interferon-mediated signaling pathway / JNK cascade / lipopolysaccharide-mediated signaling pathway / negative regulation of insulin receptor signaling pathway / response to cAMP
Similarity search - Function
Rel homology domain (RHD), DNA-binding domain / : / Nuclear factor NF-kappa-B, p105 subunit / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor ...Rel homology domain (RHD), DNA-binding domain / : / Nuclear factor NF-kappa-B, p105 subunit / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / IPT domain / SMAD/FHA domain superfamily / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p105 subunit / Transcription factor p65 / Interferon regulatory factor 3 / Interferon regulatory factor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPanne, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: An Atomic Model of the Interferon-beta Enhanceosome.
Authors: Panne, D. / Maniatis, T. / Harrison, S.C.
History
DepositionDec 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Advisory
Revision 1.4Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.6Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 400COMPOUND CHAIN A REPRESENTS A PROTEIN MADE OF THREE DIFFERENT PROTEINS FUSED TOGETHER. THE LINKERS ...COMPOUND CHAIN A REPRESENTS A PROTEIN MADE OF THREE DIFFERENT PROTEINS FUSED TOGETHER. THE LINKERS ARE DISORDERED IN THE STRUCTURE AND ARE LISTED IN SEQADV RECORDS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 36-MER
F: 34-MER
A: Transcription factor p65/Interferon regulatory factor 7/Interferon regulatory factor 3 fusion protein
B: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)117,7374
Polymers117,7374
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.222, 116.370, 134.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 36-MER


Mass: 11269.275 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 34-MER


Mass: 10255.602 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Antibody Transcription factor p65/Interferon regulatory factor 7/Interferon regulatory factor 3 fusion protein


Mass: 61032.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q04206, UniProt: Q92985, UniProt: Q14653
#4: Protein Nuclear factor NF-kappa-B p105 subunit / DNA-binding factor KBF1 / EBP-1


Mass: 35179.219 Da / Num. of mol.: 1 / Fragment: RHR region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19838
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 15% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2PEG 400011
3H2O11
4HEPES12
5PEG 400012
6H2O12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 11, 2006
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 38201 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.071 / Χ2: 1.083 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.913.50.637680.7691100
2.9-3.0213.90.4337660.8131100
3.02-3.1514.10.27137540.8521100
3.15-3.3214.30.12837921.0851100
3.32-3.5314.30.10537641.2331100
3.53-3.814.40.08537951.2691100
3.8-4.1814.50.06938171.3971100
4.18-4.7914.30.05738251.2291100
4.79-6.0314.20.04838791.0781100
6.03-5013.60.04140411.058199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→40.65 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1165152.25 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2254 6 %RANDOM
Rwork0.245 ---
obs-37592 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.848 Å2 / ksol: 0.292 e/Å3
Displacement parametersBiso mean: 64.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.98 Å20 Å20 Å2
2---1.42 Å20 Å2
3----8.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6459 1428 0 25 7912
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.42
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.504 373 6 %
Rwork0.456 5801 -
obs-6174 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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