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- PDB-1a3q: HUMAN NF-KAPPA-B P52 BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1a3q
TitleHUMAN NF-KAPPA-B P52 BOUND TO DNA
Components
  • DNA (5'-D(*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*GP*AP*TP*TP*CP*CP*CP*C)-3')
  • PROTEIN (NUCLEAR FACTOR KAPPA-B P52)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / IMMUNE RESPONSE / DNA-PROTEIN COMPLEX / TRANSCRIPTION-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 / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / 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 / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / 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 / extracellular matrix organization / response to cytokine / 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 / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor NF-kappa-B, p100 subunit / Rel homology domain (RHD), DNA-binding 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 ...Nuclear factor NF-kappa-B, p100 subunit / Rel homology domain (RHD), DNA-binding 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.1 Å
AuthorsCramer, P. / Larson, C.J. / Verdine, G.L. / Muller, C.W.
Citation
Journal: EMBO J. / Year: 1997
Title: Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution.
Authors: Cramer, P. / Larson, C.J. / Verdine, G.L. / Muller, C.W.
#1: Journal: FEBS Lett. / Year: 1997
Title: Engineering of Diffraction-Quality Crystals of the NF-kappaB P52 Homodimer:DNA Complex
Authors: Cramer, P. / Muller, C.W.
History
DepositionJan 23, 1998Deposition site: NDB / Processing site: BNL
Revision 1.0Jun 11, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*GP*AP*TP*TP*CP*CP*CP*C)-3')
A: PROTEIN (NUCLEAR FACTOR KAPPA-B P52)
B: PROTEIN (NUCLEAR FACTOR KAPPA-B P52)


Theoretical massNumber of molelcules
Total (without water)71,1154
Polymers71,1154
Non-polymers00
Water14,142785
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.200, 121.000, 134.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.998073, -0.006188, 0.061749), (-0.00671, 0.999943, -0.00826), (-0.061694, -0.008658, -0.998058)36.0579, 0.904, 2.5442
2given(-0.99376, 0.109366, -0.021925), (0.110253, 0.992911, -0.044412), (0.016913, -0.046552, -0.998773)27.2653, -1.4726, 5.1755

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*C)-3')


Mass: 3359.199 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*GP*GP*AP*TP*TP*CP*CP*CP*C)-3')


Mass: 3350.185 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (NUCLEAR FACTOR KAPPA-B P52) / NUCLEAR FACTOR KAPPA-B P52


Mass: 32202.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q00653
#4: Water ChemComp-HOH / water / WATER


Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: THE PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING THE HANGING DROP METHOD. THE RESERVOIR SOLUTION CONTAINED 5% PEG 4000, 5 MM MGSO4, 50 MM MES PH 6.0 AND 3 MM DTT. DROPS CONTAINED A 1:1 MIXTURE ...Details: THE PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING THE HANGING DROP METHOD. THE RESERVOIR SOLUTION CONTAINED 5% PEG 4000, 5 MM MGSO4, 50 MM MES PH 6.0 AND 3 MM DTT. DROPS CONTAINED A 1:1 MIXTURE OF COMPLEX SOLUTION AND RESERVOIR SOLUTION., vapor diffusion - hanging drop
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2MGSO411
3MES11
4DTT11
5PEG 400012
6MGSO412
7MES12
8DTT12
Crystal
*PLUS
Density % sol: 48.7 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlP52 homodimer1drop
25 mg/mlDNA duplex1drop
35 mMHEPES1drop
450 mM1dropNaCl
52.5 mM1dropMgCl2
61.5 mMdithiothreitol1drop
710 mMHEPES1reservoir
8100 mM1reservoirNaCl
95 mM1reservoirMgCl2
103 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 39642 / % possible obs: 91.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 39.9 Å2 / Rsym value: 6.1 / Net I/σ(I): 10.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.63 / Rsym value: 31.2 / % possible all: 78.1
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % possible obs: 91.8 % / Redundancy: 3.1 % / Num. measured all: 124281 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 78.1 % / Num. unique obs: 4127 / Num. measured obs: 8537 / Rmerge(I) obs: 0.312

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODIFIED HUMAN NF-KAPPAB P50-DNA COMPLEX, PDB ENTRY

Resolution: 2.1→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
Details: WATER MOLECULES HAVE BEEN INCLUDED IN THE MODEL WHEN A PEAK HIGHT GREATER THAN 3.0 SIGMA WAS REACHED IN A FO-FC MAP AND WHEN REASONABLE H-BONDING WAS OBSERVED (<3.5 ANGSTROM FROM ANOTHER POLAR ATOM). AT LATER STAGES, SEVERAL WATER MOLECULES WERE REMOVED WHICH SHOWED INSUFFICIENT 2FO-FC ELECTRON DENSITY. THIS PROCEDURE LEFT SEVERAL OTHER WATER MOLECULES WITHOUT APPARENT HYDROGEN BONDING. HOWEVER, THESE WATER MOLECULES WERE LEFT IN THE MODEL SINCE THEY SHOW GOOD 2FO-FC ELECTRON DENSITY. FURTHER, THEIR PRESENCE LOWERS THE FREE R-FACTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 3805 9.7 %RANDOM
Rwork0.219 ---
obs-39039 91.8 %-
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.7 Å20 Å20 Å2
2--8.4 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 445 0 785 5748
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.872.5
X-RAY DIFFRACTIONx_mcangle_it5.552.5
X-RAY DIFFRACTIONx_scbond_it5.283.5
X-RAY DIFFRACTIONx_scangle_it6.853.5
LS refinement shellResolution: 2.1→2.19 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.399 331 8.9 %
Rwork0.37 3732 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMTOPH19.PEP
X-RAY DIFFRACTION3PARAM19.SOLDNA-RNA.TOP
X-RAY DIFFRACTION4TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.64
LS refinement shell
*PLUS
Rfactor obs: 0.37

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