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- PDB-7vup: Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin k... -

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Basic information

Entry
Database: PDB / ID: 7vup
TitleStructure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment
Components
  • DNA (5'-D(*AP*AP*GP*GP*GP*GP*GP*AP*GP*TP*CP*CP*CP*CP*TP*TP*G)-3')
  • DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3')
  • Nuclear factor NF-kappa-B p52 subunit
KeywordsDNA BINDING PROTEIN/DNA / DNA-protein complex / transcription factor / TRANSCRIPTION / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / SUMOylation of immune response proteins / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / germinal center formation / 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 / SUMOylation of immune response proteins / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / germinal center formation / 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 / response to cytokine / extracellular matrix organization / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / TAK1-dependent IKK and NF-kappa-B activation / PKMTs methylate histone lysines / sequence-specific double-stranded DNA binding / rhythmic process / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
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: 3.4 Å
AuthorsMeshcheryakov, V.A. / Wang, V.Y.-F.
Funding supportMacao, 2items
OrganizationGrant numberCountry
The Science and Technology Development Fund, Macao S.A.R. (FDCT)0104/2019/A2Macao
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
DepositionNov 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3')
B: Nuclear factor NF-kappa-B p52 subunit
D: DNA (5'-D(*AP*AP*GP*GP*GP*GP*GP*AP*GP*TP*CP*CP*CP*CP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)98,5004
Polymers98,5004
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-36 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.987, 84.289, 140.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 34 - 329 / Label seq-ID: 34 - 329

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BC

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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 / 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*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3')


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

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium malonate, pH 4.0, 50mM CsCl, 2.5% PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.4→46.85 Å / Num. obs: 14272 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.998 / Net I/σ(I): 9.6
Reflection shellResolution: 3.4→3.58 Å / Num. unique obs: 2025 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a3q

1a3q


Resolution: 3.4→45.451 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.922 / SU B: 58.887 / SU ML: 0.788 / Cross valid method: FREE R-VALUE / ESU R Free: 0.622
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2858 690 4.848 %
Rwork0.2712 13543 -
all0.272 --
obs-14233 99.699 %
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: 156.456 Å2
Baniso -1Baniso -2Baniso -3
1-15.984 Å20 Å2-0 Å2
2--2.19 Å2-0 Å2
3----18.174 Å2
Refinement stepCycle: LAST / Resolution: 3.4→45.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 691 0 0 5359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135544
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154966
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0940.016497
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.6687617
X-RAY DIFFRACTIONr_angle_other_deg1.3281.58611510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7225590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.0221.328256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32515870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4841540
X-RAY DIFFRACTIONr_chiral_restr0.1150.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021208
X-RAY DIFFRACTIONr_nbd_refined0.2050.2988
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.24845
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22481
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.23066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3240.218
X-RAY DIFFRACTIONr_nbd_other0.3050.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.7060.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.5090.21
X-RAY DIFFRACTIONr_mcbond_it10.76216.1552366
X-RAY DIFFRACTIONr_mcbond_other10.76416.1542365
X-RAY DIFFRACTIONr_mcangle_it17.23124.2362954
X-RAY DIFFRACTIONr_mcangle_other17.22924.2382955
X-RAY DIFFRACTIONr_scbond_it9.38116.9743178
X-RAY DIFFRACTIONr_scbond_other9.38116.9743178
X-RAY DIFFRACTIONr_scangle_it15.36125.2334663
X-RAY DIFFRACTIONr_scangle_other15.35925.2344664
X-RAY DIFFRACTIONr_lrange_it25.429307.46421777
X-RAY DIFFRACTIONr_lrange_other25.428307.45621778
X-RAY DIFFRACTIONr_ncsr_local_group_10.1190.058790
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.118570.0501
12BX-RAY DIFFRACTIONLocal ncs0.118570.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.7230.4791670.4813165X-RAY DIFFRACTION99.7008
3.723-4.160.311350.3362851X-RAY DIFFRACTION99.5002
4.16-4.7980.2431230.2082567X-RAY DIFFRACTION99.8145
4.798-5.8620.2251170.1972192X-RAY DIFFRACTION99.8271
5.862-8.2340.272950.2091727X-RAY DIFFRACTION100
8.234-45.4510.282530.291041X-RAY DIFFRACTION99.8175

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