[English] 日本語
Yorodumi
- PDB-9bdv: NF-kappaB RelA homo-dimer bound to TA-centric kappaB DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bdv
TitleNF-kappaB RelA homo-dimer bound to TA-centric kappaB DNA
Components
  • DNA (5'-D(*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*GP*T)-3')
  • DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*AP*GP*TP*GP*AP*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 / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / 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 ...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 / TRAF6 mediated NF-kB activation / 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 / FCERI mediated NF-kB activation / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / acetaldehyde metabolic process / 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 / ankyrin repeat binding / negative regulation of protein sumoylation / 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 / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / response to UV-B / vascular endothelial growth factor signaling pathway / interleukin-1-mediated signaling pathway / 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 lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / 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 / cellular response to interleukin-1 / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of interleukin-12 production / response to interleukin-1 / negative regulation of angiogenesis / 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 / peptide binding / response to bacterium / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / protein catabolic process / response to insulin / defense response / transcription coactivator binding / negative regulation of protein catabolic process / chromatin DNA binding / cellular response to hydrogen peroxide / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nicotine / histone deacetylase binding / chromatin organization / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor binding / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBiswas, T. / Shahabi, S. / Tsodikov, O.V.
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: To Be Published
Title: Transient interactions modulate affinity of NF-kappaB transcription factors for DNA
Authors: Biswas, T. / Shandy, S. / Tsodikov, O.V. / Huang, D. / Li, T. / Wang, Y. / Wang, V. / Ghosh, G.
History
DepositionApr 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

-
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*AP*AP*TP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')
D: DNA (5'-D(*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7718
Polymers77,3874
Non-polymers3844
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-119 kcal/mol
Surface area31880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.654, 132.682, 45.663
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*AP*AP*TP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')


Mass: 5859.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*GP*T)-3')


Mass: 5788.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, MES, Spermine, beta-octylglucoside

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 57610 / % possible obs: 99.6 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.994 / Χ2: 0.047 / Net I/σ(I): 8.5 / Num. measured all: 448525
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.937.72.55829610.991199.9
1.93-1.977.81.88630010.871199.8
1.97-2.017.71.38229800.879199.8
2.01-2.067.81.18529940.91199.8
2.06-2.17.70.88329941.0581100
2.1-2.167.90.69330230.928199.9
2.16-2.217.80.60629830.903199.9
2.21-2.287.80.56630371.0871100
2.28-2.357.90.41229980.8941100
2.35-2.447.90.32130180.8961100
2.44-2.537.90.23330530.8631100
2.53-2.6580.17730180.8611100
2.65-2.7980.13730130.9361100
2.79-2.9680.130620.8961100
2.96-3.1980.07830511.0171100
3.19-3.517.90.06730981.2771100
3.51-4.027.70.05430781.1091100
4.02-5.067.50.0431270.778199.8
5.06-306.90.04431210.836194.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RAM

2ram


Resolution: 1.9→29.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.212 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23048 2577 4.9 %RANDOM
Rwork0.19109 ---
obs0.19302 49976 90.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.612 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.04 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 740 20 603 5747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125334
X-RAY DIFFRACTIONr_bond_other_d0.0090.0164403
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.6937393
X-RAY DIFFRACTIONr_angle_other_deg0.3621.56210356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.946550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47410753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02989
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9352.5432198
X-RAY DIFFRACTIONr_mcbond_other0.9342.5432198
X-RAY DIFFRACTIONr_mcangle_it1.2233.8032744
X-RAY DIFFRACTIONr_mcangle_other1.2233.8062745
X-RAY DIFFRACTIONr_scbond_it1.2613.5133136
X-RAY DIFFRACTIONr_scbond_other1.2563.5073121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6855.2234626
X-RAY DIFFRACTIONr_long_range_B_refined2.91644.3366159
X-RAY DIFFRACTIONr_long_range_B_other2.69842.6075985
X-RAY DIFFRACTIONr_rigid_bond_restr1.14639703
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 99 -
Rwork0.261 1724 -
obs--43.71 %

+
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