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- PDB-3juz: Crystal structure of a mutant of RelB dimerization domain(M5) -

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Basic information

Entry
Database: PDB / ID: 3juz
TitleCrystal structure of a mutant of RelB dimerization domain(M5)
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 / molecular replacement / Resolution: 2.51 Å
AuthorsVu, D. / Huang, D.B. / Ghosh, G.
CitationJournal: To be Published
Title: Instability of the RelB dimerization domain is functionally important
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)11,4621
Polymers11,4621
Non-polymers00
Water1,38777
1
A: Transcription factor RelB

A: Transcription factor RelB


Theoretical massNumber of molelcules
Total (without water)22,9242
Polymers22,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8730 Å2
ΔGint-62 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.840, 71.840, 60.900
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: 11461.826 Da / Num. of mol.: 1 / Fragment: dimerization domain (UNP residues 278-378) / Mutation: V314R, A324G, F358Q, L362K, N287D
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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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: 3.96 Å3/Da / Density % sol: 68.92 %
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: 2.51→30 Å / Num. all: 6155 / Num. obs: 5940 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 30.2 Å2 / Rsym value: 0.056 / Net I/σ(I): 21.3
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4 / Num. unique all: 357 / Rsym value: 0.21 / % possible all: 62

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1zk9


Resolution: 2.51→27.7 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.893 / Data cutoff high absF: 473571 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 486 8.8 %RANDOM
Rwork0.198 ---
all-5935 --
obs-5523 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.677 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 112.34 Å2 / Biso mean: 38.244 Å2 / Biso min: 15.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å23.38 Å20 Å2
2--3.47 Å20 Å2
3----6.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.51→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 0 77 880
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_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it2.421.5
X-RAY DIFFRACTIONc_mcangle_it3.92
X-RAY DIFFRACTIONc_scbond_it4.282
X-RAY DIFFRACTIONc_scangle_it6.42.5
LS refinement shellResolution: 2.51→2.67 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 47 8.5 %
Rwork0.223 503 -
all-550 -
obs--51.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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