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- PDB-2o93: Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB en... -

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Basic information

Entry
Database: PDB / ID: 2o93
TitleCrystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element
Components
  • (kappaB enhancer element, DNA 25-mer) x 2
  • actor of activated T-cells, cytoplasmic 2
KeywordsTRANSCRIPTION/DNA / IG domain / Protein-DNA complex / double helix / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


: / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / myotube cell development / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / calcineurin-NFAT signaling cascade / cartilage development / CLEC7A (Dectin-1) induces NFAT activation / positive regulation of myoblast fusion / Calcineurin activates NFAT ...: / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / myotube cell development / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / calcineurin-NFAT signaling cascade / cartilage development / CLEC7A (Dectin-1) induces NFAT activation / positive regulation of myoblast fusion / Calcineurin activates NFAT / phosphatase binding / positive regulation of B cell proliferation / 14-3-3 protein binding / cellular response to calcium ion / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / cell migration / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / transcription by RNA polymerase II / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA damage response / chromatin binding / chromatin / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / 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 / ig-like, plexins, transcription factors / IPT domain ...Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / 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 / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor of activated T-cells, cytoplasmic 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsBates, D.L. / Chen, L.
CitationJournal: Structure / Year: 2008
Title: Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element
Authors: Bates, D.L. / Barthel, K.K. / Wu, Y. / Kalhor, R. / Stroud, J.C. / Giffin, M.J. / Chen, L.
History
DepositionDec 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: kappaB enhancer element, DNA 25-mer
B: kappaB enhancer element, DNA 25-mer
L: actor of activated T-cells, cytoplasmic 2
M: actor of activated T-cells, cytoplasmic 2
O: actor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)118,0415
Polymers118,0415
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-41 kcal/mol
Surface area50290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.691, 95.299, 159.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain kappaB enhancer element, DNA 25-mer


Mass: 7681.932 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain kappaB enhancer element, DNA 25-mer


Mass: 7677.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein actor of activated T-cells, cytoplasmic 2 / T cell transcription factor NFAT1 / NFAT pre-existing subunit / NF-ATp


Mass: 34226.887 Da / Num. of mol.: 3 / Fragment: RHR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2, NFAT1, NFATP / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13469

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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 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM Hepes pH 7.0, 15mM Magnesium Acetate, 250mM Ammonium Acetate, 7.5% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Ammonium Acetate11
3Magnesium Acetate11
4Hepes11
5PEG 400012
6Ammonium Acetate12
7Magnesium Acetate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9795 Å
DetectorDetector: CCD / Date: Jul 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. obs: 26944 / % possible obs: 97.9 % / Rmerge(I) obs: 0.129 / Χ2: 2.034 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
3.05-3.160.53822691.89283.5
3.16-3.290.28725791.88296.1
3.29-3.430.30627052.10499.2
3.43-3.620.31327042.05799.9
3.62-3.840.22427242.191100
3.84-4.140.18127392.209100
4.14-4.550.12827262.218100
4.55-5.210.09827642.03100
5.21-6.550.0928001.918100
6.55-300.0529341.71999.8

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Phasing

Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P7H

1p7h


Resolution: 3.05→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2548 9.2 %RANDOM
Rwork0.225 ---
obs0.225 25518 91.8 %-
Solvent computationBsol: 35.38 Å2
Displacement parametersBiso mean: 77.72 Å2
Baniso -1Baniso -2Baniso -3
1--17.37 Å20 Å20 Å2
2--13.387 Å20 Å2
3---3.983 Å2
Refinement stepCycle: LAST / Resolution: 3.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6847 1019 0 0 7866
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.5851.5
X-RAY DIFFRACTIONc_mcangle_it6.2142
X-RAY DIFFRACTIONc_scbond_it4.4282
X-RAY DIFFRACTIONc_scangle_it7.5752.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.05-3.070.513420.401283325
3.07-3.090.363360.374324360
3.09-3.110.48420.372335377
3.11-3.140.391410.35349390
3.14-3.160.431320.363381413
3.16-3.180.383370.339389426
3.18-3.210.397380.301376414
3.21-3.230.326570.3394451
3.23-3.260.36590.267413472
3.26-3.290.249490.301427476
3.29-3.310.317450.259417462
3.31-3.340.395350.262445480
3.34-3.370.388390.271462501
3.37-3.40.332470.289445492
3.4-3.430.342390.27447486
3.43-3.470.297530.284467520
3.47-3.50.333400.297457497
3.5-3.540.353440.285484528
3.54-3.580.336580.257452510
3.58-3.620.286540.244469523
3.62-3.660.288500.258479529
3.66-3.70.292540.256474528
3.7-3.740.391640.281454518
3.74-3.790.337580.265487545
3.79-3.840.32590.251464523
3.84-3.890.299490.248461510
3.89-3.950.272580.24471529
3.95-4.010.303470.248468515
4.01-4.070.258540.218490544
4.07-4.140.28480.227473521
4.14-4.210.341520.212502554
4.21-4.280.255470.22475522
4.28-4.370.24510.189486537
4.37-4.460.281620.192499561
4.46-4.550.275540.214491545
4.55-4.660.256500.193474524
4.66-4.770.244480.188520568
4.77-4.90.273520.192477529
4.9-5.050.204500.173506556
5.05-5.210.246690.191480549
5.21-5.390.29560.189492548
5.39-5.610.241620.186502564
5.61-5.860.262630.204498561
5.86-6.170.27560.209499555
6.17-6.550.289540.227491545
6.55-7.050.262560.195516572
7.05-7.750.254580.192513571
7.75-8.840.246560.195528584
8.84-11.050.246560.17528584
11.05-300.215680.199556624
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:WATER_REP.PARAM

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