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- PDB-1le5: Crystal structure of a NF-kB heterodimer bound to an IFNb-kB -

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Basic information

Entry
Database: PDB / ID: 1le5
TitleCrystal structure of a NF-kB heterodimer bound to an IFNb-kB
Components
  • 5'-D(*AP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3'
  • 5'-D(*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*T)-3'
  • Nuclear factor NF-kappa-B p50 subunit
  • Nuclear factor NF-kappa-B p65 subunit
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTORS / Rel/NF-kB PROTEIN / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival ...SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / mammary gland involution / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / antibacterial innate immune response / Downstream TCR signaling / prolactin signaling pathway / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / positive regulation of lipid storage / cellular response to peptidoglycan / negative regulation of interleukin-12 production / ankyrin repeat binding / postsynapse to nucleus signaling pathway / negative regulation of protein sumoylation / defense response to tumor cell / cellular response to interleukin-6 / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to dsRNA / actinin binding / positive regulation of macrophage derived foam cell differentiation / response to UV-B / negative regulation of non-canonical NF-kappaB signal transduction / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / NF-kappaB complex / vascular endothelial growth factor signaling pathway / negative regulation of cytokine production / toll-like receptor 4 signaling pathway / positive regulation of amyloid-beta formation / cellular response to hepatocyte growth factor stimulus / response to cobalamin / phosphate ion binding / cellular response to cytokine stimulus / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / : / response to muramyl dipeptide / cellular response to interleukin-1 / general transcription initiation factor binding / cellular response to angiotensin / positive regulation of vascular endothelial growth factor production / positive regulation of cholesterol efflux / canonical NF-kappaB signal transduction / hair follicle development / response to amino acid / positive regulation of transcription initiation by RNA polymerase II / neuropeptide signaling pathway / lymph node development / NF-kappaB binding / RNA polymerase II core promoter sequence-specific DNA binding / response to cAMP / tumor necrosis factor-mediated signaling pathway / JNK cascade / response to muscle stretch / antiviral innate immune response / positive regulation of interleukin-12 production / Neutrophil degranulation / negative regulation of insulin receptor signaling pathway / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / liver development / response to progesterone / positive regulation of interleukin-1 beta production / response to ischemia / animal organ morphogenesis / positive regulation of interleukin-8 production / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of extrinsic apoptotic signaling pathway / B cell receptor signaling pathway / transcription coregulator activity / response to insulin / response to bacterium / protein catabolic process / defense response / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of protein catabolic process / cellular response to virus / chromatin DNA binding / positive regulation of miRNA transcription
Similarity search - Function
Rel homology domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / 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 domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / 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 / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p105 subunit / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBerkowitz, B. / Huang, D.B. / Chen-Park, F.E. / Sigler, P.B. / Ghosh, G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The X-ray crystal structure of the NF-kB p50/p65 heterodimer bound to the Interferon beta-kB site
Authors: Berkowitz, B. / Huang, D.B. / Chen-Park, F.E. / Sigler, P.B. / Ghosh, G.
History
DepositionApr 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: 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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*T)-3'
D: 5'-D(*AP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3'
G: 5'-D(*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*T)-3'
H: 5'-D(*AP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3'
A: Nuclear factor NF-kappa-B p65 subunit
B: Nuclear factor NF-kappa-B p50 subunit
E: Nuclear factor NF-kappa-B p65 subunit
F: Nuclear factor NF-kappa-B p50 subunit


Theoretical massNumber of molelcules
Total (without water)146,9908
Polymers146,9908
Non-polymers00
Water3,153175
1
C: 5'-D(*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*T)-3'
D: 5'-D(*AP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3'
A: Nuclear factor NF-kappa-B p65 subunit
B: Nuclear factor NF-kappa-B p50 subunit


Theoretical massNumber of molelcules
Total (without water)73,4954
Polymers73,4954
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*T)-3'
H: 5'-D(*AP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3'
E: Nuclear factor NF-kappa-B p65 subunit
F: Nuclear factor NF-kappa-B p50 subunit


Theoretical massNumber of molelcules
Total (without water)73,4954
Polymers73,4954
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.525, 138.015, 89.320
Angle α, β, γ (deg.)90.00, 97.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-701-

HOH

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Components

#1: DNA chain 5'-D(*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*T)-3'


Mass: 3677.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IFNb-kB DNA
#2: DNA chain 5'-D(*AP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3'


Mass: 3646.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IFNb-kB DNA
#3: Protein Nuclear factor NF-kappa-B p65 subunit / NF-kB p65


Mass: 31115.236 Da / Num. of mol.: 2 / Fragment: p65 RHR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: rela / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04207
#4: Protein Nuclear factor NF-kappa-B p50 subunit / NF-kB p50


Mass: 35056.066 Da / Num. of mol.: 2 / Fragment: p50 RHR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: nfkb1 / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25799
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM Na acatate, 50mM CaCl2, 1.0 mM Na spermine, 8% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1Na(C2H3O2)11
2CaCl211
3Na spermine11
4PEG 335011
5Na(C2H3O2)12
6CaCl212
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
250 mMsodium acetate1reservoirpH5.5
350 mM1reservoirCaCl2
40.125 %beta-octyl glucopyranoside1reservoir
51.0 mMspermine1reservoir
610 mMdithiothreitol1reservoir
77-8 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDetector: CCD / Date: Mar 26, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 42487 / Num. obs: 42487 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.4
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4242 / Rsym value: 0.032 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 99 % / Num. measured all: 280181 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VKX

1vkx


Resolution: 2.75→20 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1890 5 %RANDOM
Rwork0.26 ---
all-39958 --
obs-37688 88 %-
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9292 972 0 175 10439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2.75→2.92 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4297 240 5 %
Rwork0.407 4689 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna.paramdna-rna.top
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS

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