[English] 日本語
Yorodumi
- PDB-1le5: Crystal structure of a NF-kB heterodimer bound to an IFNb-kB -

+
Open data


ID or keywords:

Loading...

-
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


cellular response to diterpene / cellular response to glucoside / SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / 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 ...cellular response to diterpene / cellular response to glucoside / SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / 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 / antibacterial innate immune response / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / mammary gland involution / FCERI mediated NF-kB activation / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / cellular response to peptide / acetaldehyde metabolic process / cellular response to interleukin-17 / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / negative regulation of interleukin-12 production / ankyrin repeat binding / negative regulation of protein sumoylation / cellular response to dsRNA / postsynapse to nucleus signaling pathway / defense response to tumor cell / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / NF-kappaB complex / cellular response to angiotensin / response to UV-B / vascular endothelial growth factor signaling pathway / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to cytokine stimulus / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / cellular response to organic cyclic compound / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of transcription initiation by RNA polymerase II / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to amino acid / lymph node development / cellular response to interleukin-1 / JNK cascade / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / heat shock protein binding / response to muscle stretch / Neutrophil degranulation / positive regulation of interleukin-12 production / response to interleukin-1 / negative regulation of angiogenesis / protein sequestering activity / negative regulation of miRNA transcription / liver development / response to progesterone / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / response to bacterium / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / B cell receptor signaling pathway / protein catabolic process / response to insulin / defense response
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 / Immunoglobulins / Immunoglobulin-like fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

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

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more