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- PDB-2as5: Structure of the DNA binding domains of NFAT and FOXP2 bound spec... -

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Basic information

Entry
Database: PDB / ID: 2as5
TitleStructure of the DNA binding domains of NFAT and FOXP2 bound specifically to DNA.
Components
  • 5'-D(AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*TP*)-3'
  • 5'-D(TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*GP*)-3'
  • Forkhead box protein P2FOX proteins
  • Nuclear factor of activated T-cells, cytoplasmic 2NFAT
KeywordsTranscription/DNA / Forkhead Domain / RHR Domain / Rel Homology Region / IG Fold / Winged Helix-Turn-Helix / B-DNA / Transcription-DNA COMPLEX
Function / homology
Function and homology information


caudate nucleus development / putamen development / : / 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 ...caudate nucleus development / putamen development / : / 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 / cellular response to calcium ion / FCERI mediated Ca+2 mobilization / 14-3-3 protein binding / B cell receptor signaling pathway / cerebral cortex development / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell migration / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / 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 / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / FOXP, coiled-coil domain / FOXP coiled-coil domain / Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 ...: / FOXP, coiled-coil domain / FOXP coiled-coil domain / Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / 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 / Zinc finger C2H2 type domain signature. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Immunoglobulin E-set / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box protein P2 / Nuclear factor of activated T-cells, cytoplasmic 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWu, Y. / Stroud, J.C. / Borde, M. / Bates, D.L. / Guo, L. / Han, A. / Rao, A. / Chen, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: FOXP3 Controls Regulatory T Cell Function through Cooperation with NFAT.
Authors: Wu, Y. / Borde, M. / Heissmeyer, V. / Feuerer, M. / Lapan, A.D. / Stroud, J.C. / Bates, D.L. / Guo, L. / Han, A. / Ziegler, S.F. / Mathis, D. / Benoist, C. / Chen, L. / Rao, A.
History
DepositionAug 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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: 5'-D(TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*GP*)-3'
B: 5'-D(AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*TP*)-3'
C: 5'-D(TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*GP*)-3'
D: 5'-D(AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*TP*)-3'
N: Nuclear factor of activated T-cells, cytoplasmic 2
M: Nuclear factor of activated T-cells, cytoplasmic 2
F: Forkhead box protein P2
G: Forkhead box protein P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,02510
Polymers112,9768
Non-polymers492
Water2,072115
1
A: 5'-D(TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*GP*)-3'
B: 5'-D(AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*TP*)-3'
N: Nuclear factor of activated T-cells, cytoplasmic 2
F: Forkhead box protein P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5125
Polymers56,4884
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*GP*)-3'
D: 5'-D(AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*TP*)-3'
M: Nuclear factor of activated T-cells, cytoplasmic 2
G: Forkhead box protein P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5125
Polymers56,4884
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.455, 157.447, 67.666
Angle α, β, γ (deg.)90.00, 118.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules ACBD

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


Mass: 6491.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid phase synthesis
#2: DNA chain 5'-D(AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*TP*)-3'


Mass: 6389.186 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 2 types, 4 molecules NMFG

#3: Protein Nuclear factor of activated T-cells, cytoplasmic 2 / NFAT / T cell transcription factor NFAT1 / NFAT pre-existing subunit / NF-ATp


Mass: 32582.117 Da / Num. of mol.: 2 / Fragment: NFAT1 DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2, NFAT1, NFATP / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q13469
#4: Protein Forkhead box protein P2 / FOX proteins / CAG repeat protein 44 / Trinucleotide repeat-containing gene 10 protein


Mass: 11025.630 Da / Num. of mol.: 2 / Fragment: FOXP2 DNA BINDING DOMAIN / Mutation: D502I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXP2 / Plasmid: pET-30 LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O15409

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Non-polymers , 2 types, 117 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: Cacodylic Acid, PEG 4k, Sodium Chloride, Magnesium Chloride, Glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1Cacodylic Acid11
2PEG 4k11
3Sodium Chloride11
4Magnesium Chloride11
5Glycerol11
6H2O11
7Cacodylic Acid12
8PEG 4k12
9Sodium Chloride12
10Magnesium Chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.107 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 22, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.107 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 32927 / Num. obs: 31620 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.6
Reflection shellResolution: 2.7→2.8 Å / % possible all: 86.5

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1a02, chain N

1a02


Resolution: 2.7→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Data was collected to 39.3 Angstroms. Resolutions lower than 30 was not included for refinement
RfactorNum. reflectionSelection details
Rfree0.2872 2940 Random
Rwork0.2382 --
obs0.2382 29530 -
all-32927 -
Refine analyzeLuzzati coordinate error obs: 0.45 Å / Luzzati sigma a obs: 0.6 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 1710 2 115 7821
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008013
X-RAY DIFFRACTIONc_angle_deg1.30582
X-RAY DIFFRACTIONc_dihedral_angle_d22.633
X-RAY DIFFRACTIONc_improper_angle_d1.15677

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