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- PDB-3jv0: Crystal structure of a mutant of RelB dimerization domain(M6) -

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Basic information

Entry
Database: PDB / ID: 3jv0
TitleCrystal structure of a mutant of RelB dimerization domain(M6)
ComponentsTranscription factor RelB
KeywordsTRANSCRIPTION / NF-kB protein / intertwined homodimer / mutant / 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 / T-helper 1 type immune response / non-canonical NF-kappaB signal transduction / 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 / T-helper 1 type immune response / non-canonical NF-kappaB signal transduction / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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
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 / Resolution: 2.65 Å
AuthorsVu, D. / Huang, D.B. / Ghosh, G.
CitationJournal: To be Published
Title: Instability of the RelB dimerization domain is functionally importent
Authors: Vu, D. / Huang, D.B. / Ghosh, G.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)11,4961
Polymers11,4961
Non-polymers00
Water00
1
A: Transcription factor RelB

A: Transcription factor RelB


Theoretical massNumber of molelcules
Total (without water)22,9922
Polymers22,9922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8820 Å2
ΔGint-66 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.740, 71.740, 61.080
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: 11495.843 Da / Num. of mol.: 1 / Fragment: dimerization domain (UNP residues 278-378) / Mutation: V314R, A324G, F358Q, L362K, N287D, I335F
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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % PEG8000, 0.1 M 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: May 5, 2006 / Details: mirrors
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 4552 / Num. obs: 4224 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 65.8 Å2 / Rsym value: 0.094 / Net I/σ(I): 12.4
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 178 / Rsym value: 0.44 / % possible all: 38

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zk9

1zk9


Resolution: 2.65→23.48 Å / Rfactor Rfree error: 0.014 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / Data cutoff high absF: 268884 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 354 8.3 %RANDOM
Rwork0.221 ---
obs-4251 77.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.617 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 122.32 Å2 / Biso mean: 49.581 Å2 / Biso min: 23.92 Å2
Baniso -1Baniso -2Baniso -3
1-6.89 Å29.01 Å20 Å2
2--6.89 Å20 Å2
3----13.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.65→23.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 0 0 806
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_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it2.221.5
X-RAY DIFFRACTIONc_mcangle_it3.762
X-RAY DIFFRACTIONc_scbond_it3.722
X-RAY DIFFRACTIONc_scangle_it5.752.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.146 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 8 4.8 %
Rwork0.409 159 -
all-167 -
obs--18.7 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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