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- PDB-7cli: Structure of NF-kB p52 homodimer bound to P-Selectin kB DNA fragment -

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Basic information

Entry
Database: PDB / ID: 7cli
TitleStructure of NF-kB p52 homodimer bound to P-Selectin kB DNA fragment
Components
  • DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*TP*CP*AP*CP*CP*CP*CP*CP*TP*TP*C)-3')
  • DNA (5'-D(*GP*AP*AP*GP*GP*GP*GP*GP*TP*GP*AP*CP*CP*CP*CP*TP*TP*G)-3')
  • Nuclear factor NF-kappa-B p52 subunit
KeywordsDNA BINDING PROTEIN / DNA-protein complex / transcription factor / TRANSCRIPTION
Function / homology
Function and homology information


follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / Interleukin-1 processing / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation ...follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / Interleukin-1 processing / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / canonical NF-kappaB signal transduction / Purinergic signaling in leishmaniasis infection / spleen development / extracellular matrix organization / NIK-->noncanonical NF-kB signaling / response to cytokine / Dectin-1 mediated noncanonical NF-kB signaling / TAK1-dependent IKK and NF-kappa-B activation / PKMTs methylate histone lysines / 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 / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor NF-kappa-B, p100 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. ...Nuclear factor NF-kappa-B, p100 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 repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p100 subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMeshcheryakov, V.A. / Wang, V.Y.-F.
Funding supportMacao, 2items
OrganizationGrant numberCountry
The Science and Technology Development Fund, Macao S.A.R.project 0104/2019/A2Macao
The Multi-Year Research Grant from University of MacauMYRG2018-00093-FHSMacao
CitationJournal: Elife / Year: 2023
Title: Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation.
Authors: Pan, W. / Meshcheryakov, V.A. / Li, T. / Wang, Y. / Ghosh, G. / Wang, V.Y.
History
DepositionJul 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 15, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Nuclear factor NF-kappa-B p52 subunit
C: DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*TP*CP*AP*CP*CP*CP*CP*CP*TP*TP*C)-3')
B: Nuclear factor NF-kappa-B p52 subunit
D: DNA (5'-D(*GP*AP*AP*GP*GP*GP*GP*GP*TP*GP*AP*CP*CP*CP*CP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)98,5004
Polymers98,5004
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-39 kcal/mol
Surface area36480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.495, 85.370, 140.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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Components

#1: Protein Nuclear factor NF-kappa-B p52 subunit


Mass: 43732.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB2, LYT10 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q00653
#2: DNA chain DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*TP*CP*AP*CP*CP*CP*CP*CP*TP*TP*C)-3')


Mass: 5437.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*AP*AP*GP*GP*GP*GP*GP*TP*GP*AP*CP*CP*CP*CP*TP*TP*G)-3')


Mass: 5597.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M Sodium malonate, pH 4.0, 0.2M CsCl, 5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3→45.63 Å / Num. obs: 19950 / % possible obs: 95.4 % / Redundancy: 14 % / CC1/2: 0.999 / Net I/σ(I): 14.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2963 / CC1/2: 0.767 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a3q

1a3q


Resolution: 3→42.722 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.921 / SU B: 29.227 / SU ML: 0.468 / Cross valid method: FREE R-VALUE / ESU R Free: 0.455
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2753 973 4.89 %
Rwork0.236 18925 -
all0.238 --
obs-19898 94.906 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 107.301 Å2
Baniso -1Baniso -2Baniso -3
1--0.378 Å20 Å20 Å2
2--9.796 Å20 Å2
3----9.418 Å2
Refinement stepCycle: LAST / Resolution: 3→42.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4634 713 0 12 5359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125533
X-RAY DIFFRACTIONr_bond_other_d0.0020.0184859
X-RAY DIFFRACTIONr_ext_dist_refined_d0.140.016375
X-RAY DIFFRACTIONr_angle_refined_deg1.781.5757605
X-RAY DIFFRACTIONr_angle_other_deg1.4331.70111333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.34921.383253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67715864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7671539
X-RAY DIFFRACTIONr_chiral_restr0.1020.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025689
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021173
X-RAY DIFFRACTIONr_nbd_refined0.2190.21035
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.24955
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22498
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23070
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1480.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.29
X-RAY DIFFRACTIONr_nbd_other0.2330.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0740.22
X-RAY DIFFRACTIONr_mcbond_it8.3211.2252349
X-RAY DIFFRACTIONr_mcbond_other8.31711.2252348
X-RAY DIFFRACTIONr_mcangle_it13.04516.832931
X-RAY DIFFRACTIONr_mcangle_other13.04416.8312932
X-RAY DIFFRACTIONr_scbond_it7.62911.673184
X-RAY DIFFRACTIONr_scbond_other7.62811.673183
X-RAY DIFFRACTIONr_scangle_it12.28117.3034674
X-RAY DIFFRACTIONr_scangle_other12.2817.3034675
X-RAY DIFFRACTIONr_lrange_it19.595210.53121722
X-RAY DIFFRACTIONr_lrange_other19.595210.52521723
X-RAY DIFFRACTIONr_ncsr_local_group_10.2090.057628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.2850.3922320.3884578X-RAY DIFFRACTION97.8438
3.285-3.670.312060.2793933X-RAY DIFFRACTION93.1578
3.67-4.2330.2681940.223629X-RAY DIFFRACTION96.6136
4.233-5.1730.2281690.1613069X-RAY DIFFRACTION96.1116
5.173-7.2680.2611140.1972366X-RAY DIFFRACTION92.9884
7.268-42.7220.272570.2721346X-RAY DIFFRACTION87.7423

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