[English] 日本語
Yorodumi
- PDB-2v2t: X-ray structure of a NF-kB p50-RelB-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v2t
TitleX-ray structure of a NF-kB p50-RelB-DNA complex
Components
  • 5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*CP*CP*CP)-3'
  • NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT
  • TRANSCRIPTION FACTOR RELB
KeywordsTRANSCRIPTION / 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL / AQUIFEX AEOLICUS / NUCLEOTIDE-BINDING / ISOPRENE BIOSYNTHESIS / KINASE / TRANSFERASE / ATP-BINDING / NON-MEVALONATE
Function / homology
Function and homology information


cellular response to diterpene / cellular response to glucoside / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / 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 hyaluronan biosynthetic process ...cellular response to diterpene / cellular response to glucoside / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / 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 hyaluronan biosynthetic process / PKMTs methylate histone lysines / mammary gland involution / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / NF-kB is activated and signals survival / cellular response to carbohydrate stimulus / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / myeloid dendritic cell differentiation / lymphocyte differentiation / TAK1-dependent IKK and NF-kappa-B activation / cellular response to interleukin-17 / Activation of NF-kappaB in B cells / NF-kappaB p50/p65 complex / cellular response to peptide / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / antibacterial innate immune response / Downstream TCR signaling / negative regulation of interleukin-12 production / CD209 (DC-SIGN) signaling / T-helper 1 type immune response / positive regulation of lipid storage / signal transduction involved in regulation of gene expression / negative regulation of interferon-beta production / cellular response to interleukin-6 / positive regulation of macrophage derived foam cell differentiation / lymph node development / cellular response to dsRNA / actinin binding / cellular response to osmotic stress / positive regulation of miRNA metabolic process / negative regulation of cytokine production / antigen processing and presentation / T-helper 1 cell differentiation / non-canonical NF-kappaB signal transduction / NF-kappaB complex / transcription repressor complex / cellular response to cytokine stimulus / response to muscle stretch / cellular response to angiotensin / cellular response to interleukin-1 / positive regulation of cholesterol efflux / positive regulation of transcription initiation by RNA polymerase II / JNK cascade / cis-regulatory region sequence-specific DNA binding / canonical NF-kappaB signal transduction / cellular response to brain-derived neurotrophic factor stimulus / heat shock protein binding / response to cytokine / Neutrophil degranulation / negative regulation of cytokine production involved in inflammatory response / gene expression / B cell receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to tumor necrosis factor / circadian regulation of gene expression / cellular response to virus / cellular response to mechanical stimulus / negative regulation of inflammatory response / protein sequestering activity / cellular response to nicotine / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / transcription coregulator activity / positive regulation of inflammatory response / sequence-specific double-stranded DNA binding / positive regulation of canonical Wnt signaling pathway / MAPK cascade / cellular response to lipopolysaccharide / response to oxidative stress / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / centrosome / positive regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process
Similarity search - Function
Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / Rel homology domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / NF-kappa-B/Dorsal / Rel homology domain, conserved site ...Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / Rel homology domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / 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 repeat profile. / Ankyrin repeats (3 copies) / 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 RelB
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsMoorthy, A.K. / Huang, D.B. / Wang, V.Y. / Vu, D. / Ghosh, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: X-Ray Structure of a NF-kappaB p50/Relb/DNA Complex Reveals Assembly of Multiple Dimers on Tandem kappaB Sites.
Authors: Moorthy, A.K. / Huang, D.B. / Wang, V.Y. / Vu, D. / Ghosh, G.
History
DepositionJun 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSCRIPTION FACTOR RELB
B: NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT
C: 5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*CP*CP*CP)-3'
D: 5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*CP*CP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)75,9854
Polymers75,9854
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-2.9 kcal/mol
Surface area39620 Å2
MethodPQS
Unit cell
Length a, b, c (Å)91.440, 91.440, 419.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein TRANSCRIPTION FACTOR RELB / RELB


Mass: 32604.146 Da / Num. of mol.: 1 / Fragment: RESIDUES 91-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: NF-KB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q04863
#2: Protein NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT / DNA-BINDING FACTOR KBF1 / EBP-1 / NF-KAPPA-B1 P84/NF-KAPPA-B1 P98 / P50


Mass: 36712.926 Da / Num. of mol.: 1
Fragment: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT, RESIDUES 38-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: NF-KB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25799
#3: DNA chain 5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*CP*CP*CP)-3'


Mass: 3334.186 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 7
Details: 5% PEG3350 100 MM NACITRATE 1MM SPERMINE 5MM DTT, pH 7

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.05
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 3.04→30 Å / Num. obs: 19931 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 86 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12
Reflection shellResolution: 3.04→3.15 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 91

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VKX

1vkx


Resolution: 3.05→19.9 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 89352.41 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 916 4.8 %RANDOM
Rwork0.238 ---
obs0.238 19087 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.5829 Å2 / ksol: 0.212846 e/Å3
Displacement parametersBiso mean: 74 Å2
Baniso -1Baniso -2Baniso -3
1-10.87 Å220.2 Å20 Å2
2--10.87 Å20 Å2
3----21.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.05→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 442 0 34 5134
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.05→3.24 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 117 4.5 %
Rwork0.329 2502 -
obs--78.6 %
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

+
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