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- PDB-3jv6: Crystal structure of the dimerization domains p52 and RelB -

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Basic information

Entry
Database: PDB / ID: 3jv6
TitleCrystal structure of the dimerization domains p52 and RelB
Components
  • Nuclear factor NF-kappa-B p100 subunit
  • Transcription factor RelB
KeywordsTRANSCRIPTION / NF-kB protein / Heterodimer / RelB and p52 / Activator / Nucleus / Phosphoprotein / Transcription regulation / ANK repeat / DNA-binding / Isopeptide bond
Function / homology
Function and homology information


follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / SUMOylation of immune response proteins / 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 / T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling ...follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / SUMOylation of immune response proteins / 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 / T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / PKMTs methylate histone lysines / TAK1-dependent IKK and NF-kappa-B activation / lymphocyte differentiation / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / germinal center formation / 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 / lymph node development / spleen development / transcription repressor complex / extracellular matrix organization / response to cytokine / circadian regulation of gene expression / rhythmic process / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / 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 / regulation of DNA-templated transcription / protein kinase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor RelB / Nuclear factor NF-kappa-B, p100 subunit / 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. ...Transcription factor RelB / Nuclear factor NF-kappa-B, p100 subunit / 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 / 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 repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transcription factor RelB / Nuclear factor NF-kappa-B p100 subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.78 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 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 1.2Mar 27, 2013Group: Database references
Revision 1.3Sep 4, 2013Group: Database references
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor RelB
B: Nuclear factor NF-kappa-B p100 subunit
C: Transcription factor RelB
D: Nuclear factor NF-kappa-B p100 subunit
E: Transcription factor RelB
F: Nuclear factor NF-kappa-B p100 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,37515
Polymers71,5116
Non-polymers8659
Water2,630146
1
A: Transcription factor RelB
B: Nuclear factor NF-kappa-B p100 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1255
Polymers23,8372
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-42 kcal/mol
Surface area11550 Å2
MethodPISA
2
C: Transcription factor RelB
D: Nuclear factor NF-kappa-B p100 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1255
Polymers23,8372
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-40 kcal/mol
Surface area11460 Å2
MethodPISA
3
E: Transcription factor RelB
F: Nuclear factor NF-kappa-B p100 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1255
Polymers23,8372
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-40 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.335, 141.144, 168.986
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A,C,E, using restrain
22chain B,D,F, using restrain

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111AA248 - 344248 - 344
121CC248 - 344248 - 344
131EE248 - 344248 - 344
212BB225 - 264225 - 264
222BB269 - 327269 - 327
232DD225 - 264225 - 264
242DD269 - 327269 - 327
252FF225 - 264225 - 264
262FF269 - 327269 - 327

NCS ensembles :
ID
1
2

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Components

#1: Protein Transcription factor RelB


Mass: 11405.868 Da / Num. of mol.: 3 / Fragment: dimerization domain (UNP residues 278-378)
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: Protein Nuclear factor NF-kappa-B p100 subunit / DNA-binding factor KBF2 / Nuclear factor NF-kappa-B p52 subunit


Mass: 12430.976 Da / Num. of mol.: 3 / Fragment: dimerization domain (UNP residues 225-331)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: p52 / Plasmid: PET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9WTK5
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 5.27 Å3/Da / Density % sol: 76.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, ammonium sulfate, 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: Oct 15, 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: 2.8→30 Å / Num. all: 33723 / Num. obs: 30666 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.105 / Net I/σ(I): 8.1
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2436 / Rsym value: 0.554 / % possible all: 64

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→29.63 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.51 / FOM work R set: 0.702 / Data cutoff high absF: 136706 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1338 5 %RANDOM
Rwork0.205 ---
obs-26839 70.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.256 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso max: 140 Å2 / Biso mean: 74.11 Å2 / Biso min: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--33.02 Å20 Å20 Å2
2--67.79 Å20 Å2
3----34.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a1.1 Å1.19 Å
Refinement stepCycle: LAST / Resolution: 2.78→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 45 146 5191
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.87
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11CX-RAY DIFFRACTION0.07restrain100
11EX-RAY DIFFRACTION0.088restrain100
22FX-RAY DIFFRACTION0.057restrain100
LS refinement shellResolution: 2.78→2.91 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.496 85 5.2 %
Rwork0.445 1561 -
all-1646 -
obs--35 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2as.paramas.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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