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- PDB-3jv4: Crystal structure of the dimerization domains p50 and RelB -

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Basic information

Entry
Database: PDB / ID: 3jv4
TitleCrystal structure of the dimerization domains p50 and RelB
Components
  • Nuclear factor NF-kappa-B p105 subunit
  • Transcription factor RelB
KeywordsTRANSCRIPTION / NF-kB protein / Heterodimer / RelB and p50 / Activator / Nucleus / Phosphoprotein / Transcription regulation / ANK repeat / Apoptosis / DNA-binding / S-nitrosylation
Function / homology
Function and homology information


cellular response to diterpene / cellular response to glucoside / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling ...cellular response to diterpene / cellular response to glucoside / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / antibacterial innate immune response / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / mammary gland involution / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / lymphocyte differentiation / cellular response to peptide / Downstream TCR signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / negative regulation of interleukin-12 production / negative regulation of interferon-beta production / cellular response to dsRNA / cellular response to osmotic stress / cellular response to interleukin-6 / actinin binding / cellular response to angiotensin / negative regulation of cytokine production / positive regulation of miRNA metabolic process / T-helper 1 type immune response / non-canonical NF-kappaB signal transduction / cellular response to cytokine stimulus / cellular response to organic cyclic compound / antigen processing and presentation / positive regulation of transcription initiation by RNA polymerase II / canonical NF-kappaB signal transduction / lymph node development / cellular response to interleukin-1 / JNK cascade / cellular response to brain-derived neurotrophic factor stimulus / heat shock protein binding / response to muscle stretch / transcription repressor complex / Neutrophil degranulation / protein sequestering activity / response to cytokine / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / circadian regulation of gene expression / response to organic cyclic compound / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / cellular response to mechanical stimulus / cellular response to nicotine / positive regulation of canonical Wnt signaling pathway / MAPK cascade / sequence-specific double-stranded DNA binding / gene expression / cellular response to tumor necrosis factor / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to oxidative stress / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / 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 / negative regulation of gene expression / innate immune response / negative regulation of DNA-templated transcription / centrosome / synapse / apoptotic process / chromatin binding / chromatin / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding
Similarity search - Function
Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / : / Nuclear factor NF-kappa-B, p105 subunit / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain ...Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation 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 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
Nuclear factor NF-kappa-B p105 subunit / Transcription factor RelB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.15 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor RelB
B: Nuclear factor NF-kappa-B p105 subunit
C: Transcription factor RelB
D: Nuclear factor NF-kappa-B p105 subunit
E: Transcription factor RelB
F: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)74,3766
Polymers74,3766
Non-polymers00
Water0
1
A: Transcription factor RelB
B: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)24,7922
Polymers24,7922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transcription factor RelB
D: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)24,7922
Polymers24,7922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Transcription factor RelB
F: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)24,7922
Polymers24,7922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.173, 106.173, 143.778
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
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-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEULEULEUAA281 - 3764 - 99
121LEULEULEULEUCC281 - 3764 - 99
131LEULEULEULEUEE281 - 3764 - 99
212ASNASNGLUGLUBB247 - 2853 - 41
232TRPTRPGLUGLUBB292 - 35048 - 106
242ASNASNGLUGLUDD247 - 2853 - 41
252TRPTRPGLUGLUDD292 - 35048 - 106
262ASNASNGLUGLUFF247 - 2853 - 41
272TRPTRPGLUGLUFF292 - 35048 - 106

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 p105 subunit / DNA-binding factor KBF1 / EBP-1 / NF-kappa-B1 p84/NF-kappa-B1 p98 / Nuclear factor NF-kappa-B p50 subunit


Mass: 13386.117 Da / Num. of mol.: 3 / Fragment: dimerization domain (UNP residues 245-359)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: p50 / Plasmid: PET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P25799

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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: 3.15 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, 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: Mar 5, 2007 / 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: 3.15→25 Å / Num. all: 15163 / Num. obs: 13637 / % possible obs: 82 % / Observed criterion σ(I): 1 / Redundancy: 9 % / Rsym value: 0.077 / Net I/σ(I): 8.4
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2417 / Rsym value: 0.53 / % possible all: 77

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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 / Resolution: 3.15→29.76 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.836 / Data cutoff high absF: 32597 / 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
Rfree0.28 686 5 %RANDOM
Rwork0.225 ---
all-15139 --
obs-13629 81.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.286 Å2 / ksol: 0.275 e/Å3
Displacement parametersBiso max: 140 Å2 / Biso mean: 89.462 Å2 / Biso min: 30.27 Å2
Baniso -1Baniso -2Baniso -3
1-7.68 Å2-11.47 Å20 Å2
2--7.68 Å20 Å2
3----15.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.15→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 0 0 5185
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.98
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11CX-RAY DIFFRACTION0.086restrain100
11EX-RAY DIFFRACTION0.084restrain100
22FX-RAY DIFFRACTION0.099restrain100
LS refinement shellResolution: 3.15→3.29 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.356 59 5.7 %
Rwork0.308 980 -
all-1039 -
obs--50.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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