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- PDB-1owr: CRYSTAL STRUCTURE OF HUMAN NFAT1 BOUND MONOMERICALLY TO DNA -

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Basic information

Entry
Database: PDB / ID: 1owr
TitleCRYSTAL STRUCTURE OF HUMAN NFAT1 BOUND MONOMERICALLY TO DNA
Components
  • NFAT1 Monomeric Binding Site, Minus Strand
  • NFAT1 Monomeric Binding Site, Plus Strand
  • Nuclear factor of activated T-cells, cytoplasmic 2NFAT
KeywordsTRANSCRIPTION/DNA / BETA BARREL / PROTEIN-DNA COMPLEX / DOUBLE HELIX / BINARY / MONOMER / PSEUDO-CONTINUOUS / 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 / cellular response to calcium ion / FCERI mediated Ca+2 mobilization / 14-3-3 protein binding / B cell receptor signaling pathway / 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 / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / 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 Å
AuthorsStroud, J.C. / Chen, L.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure of NFAT Bound to DNA as a Monomer
Authors: Stroud, J.C. / Chen, L.
History
DepositionMar 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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: NFAT1 Monomeric Binding Site, Plus Strand
B: NFAT1 Monomeric Binding Site, Minus Strand
C: NFAT1 Monomeric Binding Site, Plus Strand
D: NFAT1 Monomeric Binding Site, Minus Strand
E: NFAT1 Monomeric Binding Site, Plus Strand
F: NFAT1 Monomeric Binding Site, Minus Strand
G: NFAT1 Monomeric Binding Site, Plus Strand
H: NFAT1 Monomeric Binding Site, Minus Strand
M: Nuclear factor of activated T-cells, cytoplasmic 2
N: Nuclear factor of activated T-cells, cytoplasmic 2
P: Nuclear factor of activated T-cells, cytoplasmic 2
Q: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)165,95512
Polymers165,95512
Non-polymers00
Water0
1
A: NFAT1 Monomeric Binding Site, Plus Strand
B: NFAT1 Monomeric Binding Site, Minus Strand
M: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)41,4893
Polymers41,4893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NFAT1 Monomeric Binding Site, Plus Strand
D: NFAT1 Monomeric Binding Site, Minus Strand
N: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)41,4893
Polymers41,4893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: NFAT1 Monomeric Binding Site, Plus Strand
F: NFAT1 Monomeric Binding Site, Minus Strand
P: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)41,4893
Polymers41,4893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: NFAT1 Monomeric Binding Site, Plus Strand
H: NFAT1 Monomeric Binding Site, Minus Strand
Q: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)41,4893
Polymers41,4893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.646, 94.849, 112.788
Angle α, β, γ (deg.)90.00, 104.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a single protein polymer of the NFAT1 RHR in complex with a double stranded piece of DNA of 13 base pairs with a 2 base overhang at the 5' end. There are 4 such biological units in the asymmetric unit.

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Components

#1: DNA chain
NFAT1 Monomeric Binding Site, Plus Strand


Mass: 4657.059 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The plus strand of the NFAT1 monomeric binding site was chemically synthesized
#2: DNA chain
NFAT1 Monomeric Binding Site, Minus Strand


Mass: 4518.959 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The minus strand of the NFAT1 monomeric binding site was chemically synthesized
#3: Protein
Nuclear factor of activated T-cells, cytoplasmic 2 / NFAT / T cell transcription factor NFAT1 / NFAT pre-existing subunit / NF-ATp


Mass: 32312.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2 OR NFAT1 OR NFATP / 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: 3.26 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: sodium cacodylate, magnesium chloride, peg 3000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2magnesium chloride11
3peg 300011
4H2O11
5sodium cacodylate12
6magnesium chloride12
7peg 300012
8H2O12
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
21 mMdithiothreitol1drop
3100 mM1dropNaCl
450 mMsodium cacodylate1reservoirpH6.3
510 mM1reservoirMgCl2
616 %(w/v)PEG30001reservoir
71
81

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 39696 / Num. obs: 39696 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.6
Reflection shellResolution: 3→3.07 Å / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 97.3 % / Mean I/σ(I) obs: 2.13

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A02

1a02


Resolution: 3→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Starting model is the structure of the DNA binding domains of nfat, fos and jun bound to DNA without RHR-N bound to b-form dsDNA
RfactorNum. reflectionSelection details
Rfree0.2731 3180 RANDOM
Rwork0.2411 --
obs-34257 -
Solvent computationBsol: 16.8187 Å2 / ksol: 0.273655 e/Å3
Displacement parametersBiso mean: 66.8 Å2
Baniso -1Baniso -2Baniso -3
1--19.258 Å20 Å24.074 Å2
2--7.922 Å20 Å2
3---11.336 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9000 2436 0 0 11436
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.651.5
X-RAY DIFFRACTIONc_mcangle_it3.5612
X-RAY DIFFRACTIONc_scbond_it4.4212
X-RAY DIFFRACTIONc_scangle_it6.0362.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.402 317 -
Rwork0.39 --
obs--82.3 %
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / % reflection Rfree: 7.7 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / Rfactor Rwork: 0.334

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