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- PDB-3jss: Crystal structure of a mutant RelB dimerization domain -

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Basic information

Entry
Database: PDB / ID: 3jss
TitleCrystal structure of a mutant RelB dimerization domain
ComponentsTranscription factor RelB
KeywordsTRANSCRIPTION / NF-kB / intertwined dimer / Activator / Nucleus / Phosphoprotein / Transcription regulation
Function / homology
Function and homology information


T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / negative regulation of interferon-beta production / cellular response to osmotic stress / non-canonical NF-kappaB signal transduction / T-helper 1 type immune response / antigen processing and presentation ...T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / negative regulation of interferon-beta production / cellular response to osmotic stress / non-canonical NF-kappaB signal transduction / T-helper 1 type immune response / antigen processing and presentation / canonical NF-kappaB signal transduction / transcription repressor complex / response to cytokine / circadian regulation of gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / negative regulation of DNA-templated transcription / centrosome / synapse / chromatin / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / 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 ...Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transcription factor RelB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsVu, D. / Huang, D.B. / Ghosh, G.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: A structural basis for selective dimerization by NF-kappa B RelB.
Authors: Vu, D. / Huang, D.B. / Vemu, A. / Ghosh, G.
History
DepositionSep 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Sep 4, 2013Group: Database references
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Oct 13, 2021Group: 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 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor RelB


Theoretical massNumber of molelcules
Total (without water)11,4611
Polymers11,4611
Non-polymers00
Water00
1
A: Transcription factor RelB

A: Transcription factor RelB


Theoretical massNumber of molelcules
Total (without water)22,9222
Polymers22,9222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8690 Å2
ΔGint-60 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.730, 71.730, 60.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Transcription factor RelB


Mass: 11460.842 Da / Num. of mol.: 1 / Fragment: dimerization domain (UNP residues 278-378) / Mutation: V314R, A324G, F358Q, L362K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RelB / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q04863

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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: 3.94 Å3/Da / Density % sol: 68.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG800, 0.1M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2006 / Details: mirros
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 5318 / Num. obs: 4987 / % possible obs: 85 % / Observed criterion σ(I): 1 / Redundancy: 12 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.8 / Num. unique all: 288 / % possible all: 50

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→23.48 Å / Rfactor Rfree error: 0.013 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 362431 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.259 382 8.5 %RANDOM
Rwork0.218 ---
obs-4503 77.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.682 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 114.1 Å2 / Biso mean: 39.386 Å2 / Biso min: 7.71 Å2
Baniso -1Baniso -2Baniso -3
1-5.89 Å29.08 Å20 Å2
2--5.89 Å20 Å2
3----11.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→23.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 0 0 803
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it4.81.5
X-RAY DIFFRACTIONc_mcangle_it6.662
X-RAY DIFFRACTIONc_scbond_it6.942
X-RAY DIFFRACTIONc_scangle_it9.12.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 33 10.7 %
Rwork0.257 275 -
all-308 -
obs--32 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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