[English] 日本語
Yorodumi
- PDB-9e6w: NF-kappaB RelA homo-dimer bound to a kappaB site of Cxcl2 gene -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e6w
TitleNF-kappaB RelA homo-dimer bound to a kappaB site of Cxcl2 gene
Components
  • DNA (5'-D(P*AP*CP*TP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*AP*GP*TP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*AP*GP*T)-3')
  • Transcription factor p65
KeywordsDNA BINDING PROTEIN/DNA / RelA / kappaB DNA / Promoter / Transcription / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / Interleukin-1 processing / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / positive regulation of Schwann cell differentiation / PKMTs methylate histone lysines / NF-kB is activated and signals survival / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells ...SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / Interleukin-1 processing / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / positive regulation of Schwann cell differentiation / PKMTs methylate histone lysines / NF-kB is activated and signals survival / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / TAK1-dependent IKK and NF-kappa-B activation / Activation of NF-kappaB in B cells / prolactin signaling pathway / positive regulation of chondrocyte differentiation / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / Downstream TCR signaling / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / defense response to tumor cell / positive regulation of T cell receptor signaling pathway / signal transduction involved in regulation of gene expression / cellular response to interleukin-6 / negative regulation of non-canonical NF-kappaB signal transduction / actinin binding / positive regulation of miRNA metabolic process / response to UV-B / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / vascular endothelial growth factor signaling pathway / non-canonical NF-kappaB signal transduction / NF-kappaB complex / phosphate ion binding / cellular response to lipoteichoic acid / response to muramyl dipeptide / cellular response to angiotensin / hair follicle development / positive regulation of vascular endothelial growth factor production / cellular response to interleukin-1 / general transcription initiation factor binding / NF-kappaB binding / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to muscle stretch / positive regulation of interleukin-12 production / peptide binding / negative regulation of insulin receptor signaling pathway / negative regulation of cytokine production involved in inflammatory response / response to cytokine / negative regulation of miRNA transcription / negative regulation of angiogenesis / response to interleukin-1 / antiviral innate immune response / : / animal organ morphogenesis / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / positive regulation of interleukin-1 beta production / negative regulation of extrinsic apoptotic signaling pathway / response to bacterium / RNA polymerase II transcription regulatory region sequence-specific DNA binding / liver development / defense response / neuropeptide signaling pathway / negative regulation of protein catabolic process / chromatin DNA binding / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nicotine / positive regulation of miRNA transcription / positive regulation of interleukin-6 production / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to tumor necrosis factor / transcription coactivator binding / histone deacetylase binding / cellular response to hydrogen peroxide / cytokine-mediated signaling pathway / chromatin organization / cellular response to lipopolysaccharide / regulation of inflammatory response / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
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. ...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 / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBiswas, T. / Shahabi, S. / Ghosh, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM085490-11 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Teamwork of clustered low-affinity kappa B sites and accessory factors regulates transcriptional strength of NF-kappa B RelA dimers.
Authors: Shahabi, S. / Biswas, T. / Shen, Y. / Sanahmadi, R. / Zou, Y. / Ghosh, G.
History
DepositionOct 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription factor p65
B: Transcription factor p65
C: DNA (5'-D(P*AP*CP*TP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*AP*GP*TP*GP*A)-3')
D: DNA (5'-D(P*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)76,7714
Polymers76,7714
Non-polymers00
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-45 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.789, 133.081, 45.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 32869.223 Da / Num. of mol.: 2 / Fragment: residues 19-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rela, Nfkb3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04207
#2: DNA chain DNA (5'-D(P*AP*CP*TP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*AP*GP*TP*GP*A)-3')


Mass: 5522.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(P*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*AP*GP*T)-3')


Mass: 5509.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Tris HCl 25mM pH 7.5, NaCl 50 mM, DTT 1 mM, MES 50 mM pH 5.5, CaCl2 2 mM, Spermidine 1 mM, b-D-octylglucopyranoside 0.05%, Ammonium chloride 50 mM, PEG3350 14%

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 46623 / % possible obs: 99.4 % / Redundancy: 13 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Χ2: 0.858 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.03-2.0710.61.71823260.6810.90.5471.8061.19899.5
2.07-2.111.42.0422490.7920.940.6242.1360.69299.1
2.1-2.1411.31.54722690.8450.9570.4731.6210.62696.9
2.14-2.1913.31.18122680.9090.9760.3311.2280.63399.5
2.19-2.2313.21.36823070.9040.9750.3851.4220.77299.6
2.23-2.2912.90.94423140.9120.9770.2730.9831.29699.7
2.29-2.3414.10.822890.9490.9870.2170.8290.63599.8
2.34-2.4113.90.62923300.9680.9920.1720.6530.65199.9
2.41-2.4813.90.4923000.9750.9940.1340.5080.64599.7
2.48-2.5613.70.38923150.9820.9950.1070.4040.64499.8
2.56-2.6513.30.29223470.9910.9980.0820.3030.71199.8
2.65-2.76130.23623140.9930.9980.0670.2460.97399.9
2.76-2.8812.80.15123280.9960.9990.0440.1580.707100
2.88-3.0311.90.11223030.9970.9990.0330.1170.75998.1
3.03-3.2213.10.08123290.9980.9990.0230.0840.81698.4
3.22-3.4714.10.07323510.99910.020.0761.193100
3.47-3.8213.90.06223650.99910.0170.0641.188100
3.82-4.3713.50.05123870.99910.0140.0531.244100
4.37-5.5112.60.04424250.99810.0130.0460.989100
5.51-5012.50.03825070.9970.9990.0110.040.76397.7

-
Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→37.48 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2829 1752 4.9 %
Rwork0.2438 --
obs0.2457 35763 76.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 738 0 264 5386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045315
X-RAY DIFFRACTIONf_angle_d0.7187359
X-RAY DIFFRACTIONf_dihedral_angle_d21.925969
X-RAY DIFFRACTIONf_chiral_restr0.046793
X-RAY DIFFRACTIONf_plane_restr0.007862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.10.3504390.3021595X-RAY DIFFRACTION18
2.1-2.160.3007520.2824886X-RAY DIFFRACTION26
2.16-2.230.3715570.2961423X-RAY DIFFRACTION42
2.23-2.310.3474940.33851772X-RAY DIFFRACTION53
2.31-2.40.35021270.30082365X-RAY DIFFRACTION70
2.4-2.510.34051440.29912927X-RAY DIFFRACTION86
2.51-2.640.36841750.29533343X-RAY DIFFRACTION99
2.64-2.810.38691890.29943374X-RAY DIFFRACTION100
2.81-3.020.31591660.28343436X-RAY DIFFRACTION100
3.02-3.330.26241640.24473337X-RAY DIFFRACTION98
3.33-3.810.2651970.23433455X-RAY DIFFRACTION100
3.81-4.790.22561720.1943468X-RAY DIFFRACTION100
4.8-37.480.23111760.19743630X-RAY DIFFRACTION99

+
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