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- PDB-7vuq: Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin ... -

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Basic information

Entry
Database: PDB / ID: 7vuq
TitleStructure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment
Components
  • DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*TP*TP*AP*CP*CP*CP*CP*CP*TP*T)-3')
  • DNA (5'-D(*GP*AP*AP*GP*GP*GP*GP*GP*TP*AP*AP*CP*CP*CP*CP*TP*TP*G)-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: 3.1 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,4994
Polymers98,4994
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-43 kcal/mol
Surface area36190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.453, 84.627, 139.427
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
11B
21A
32D
42C

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
111THRTHRVALVALBA34 - 32934 - 329
221THRTHRVALVALAC34 - 32934 - 329
332DGDGDTDTDB1 - 161 - 16
442DCDCDTDTCD1 - 161 - 16

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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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(*GP*AP*AP*GP*GP*GP*GP*GP*TP*AP*AP*CP*CP*CP*CP*TP*TP*G)-3')


Mass: 5581.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*TP*TP*AP*CP*CP*CP*CP*CP*TP*T)-3')


Mass: 5452.529 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: 51.37 %
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: 3.1→46.48 Å / Num. obs: 18756 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 3.1→3.27 Å / Num. unique obs: 2690 / CC1/2: 0.934

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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: 3.1→40.003 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.2 / SU B: 33.276 / SU ML: 0.496 / Average fsc free: 0.7887 / Average fsc work: 0.8027 / Cross valid method: FREE R-VALUE / ESU R Free: 0.433
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2487 983 5.256 %
Rwork0.2243 17720 -
all0.226 --
obs-18703 99.76 %
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: 131.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.769 Å20 Å2-0 Å2
2--12.045 Å2-0 Å2
3----13.814 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 713 0 0 5381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135569
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154978
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0910.016501
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.6697656
X-RAY DIFFRACTIONr_angle_other_deg1.371.58511539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3195590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03121.328256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.80615870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4331540
X-RAY DIFFRACTIONr_chiral_restr0.1240.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025781
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021210
X-RAY DIFFRACTIONr_nbd_refined0.2190.21078
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.24903
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22490
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23208
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.216
X-RAY DIFFRACTIONr_nbd_other0.230.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3140.23
X-RAY DIFFRACTIONr_mcbond_it9.68813.5952366
X-RAY DIFFRACTIONr_mcbond_other9.66613.5952365
X-RAY DIFFRACTIONr_mcangle_it14.80620.3942954
X-RAY DIFFRACTIONr_mcangle_other14.80320.3952955
X-RAY DIFFRACTIONr_scbond_it9.18414.1033203
X-RAY DIFFRACTIONr_scbond_other9.18314.1043204
X-RAY DIFFRACTIONr_scangle_it14.35320.9334702
X-RAY DIFFRACTIONr_scangle_other14.35120.9344703
X-RAY DIFFRACTIONr_lrange_it21.025255.77722027
X-RAY DIFFRACTIONr_lrange_other21.025255.77622028
X-RAY DIFFRACTIONr_ncsr_local_group_10.160.058410
X-RAY DIFFRACTIONr_ncsr_local_group_20.2130.051157
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.160410.05008
12AX-RAY DIFFRACTIONLocal ncs0.160410.05008
23DX-RAY DIFFRACTIONLocal ncs0.21320.05008
24CX-RAY DIFFRACTIONLocal ncs0.21320.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.1-3.3940.4282290.40141450.40243870.450.48499.70370.347
3.394-3.7910.3222060.29937550.339680.7740.79299.82360.264
3.791-4.3710.241810.21133450.21235300.9260.92599.88670.186
4.371-5.3370.2551550.16928660.17330230.9320.9599.93380.159
5.337-7.4820.2411440.19622410.19923860.930.94699.95810.192
7.482-40.0030.156680.20413680.20214400.9820.95699.72220.211

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