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- PDB-8r3f: C-terminal Rel-homology Domain of NFAT1 -

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Basic information

Entry
Database: PDB / ID: 8r3f
TitleC-terminal Rel-homology Domain of NFAT1
ComponentsNuclear factor of activated T-cells, cytoplasmic 2
KeywordsTRANSCRIPTION / NFAT1 / Transcription Factor / Fragment
Function / homology
Function and homology information


lncRNA transcription / 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 / positive regulation of myoblast fusion / CLEC7A (Dectin-1) induces NFAT activation / Calcineurin activates NFAT ...lncRNA transcription / 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 / positive regulation of myoblast fusion / CLEC7A (Dectin-1) induces NFAT activation / Calcineurin activates NFAT / phosphatase binding / positive regulation of B cell proliferation / 14-3-3 protein binding / FCERI mediated Ca+2 mobilization / cellular response to calcium ion / 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 / molecular adaptor activity / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / ribonucleoprotein complex / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear factor of activated T cells (NFAT) / 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 ...Nuclear factor of activated T cells (NFAT) / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Nuclear factor of activated T-cells, cytoplasmic 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZak, K.M. / Boettcher, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Arch Pharm / Year: 2024
Title: Ligandability assessment of the C-terminal Rel-homology domain of NFAT1.
Authors: Bottcher, J. / Fuchs, J.E. / Mayer, M. / Kahmann, J. / Zak, K.M. / Wunberg, T. / Woehrle, S. / Kessler, D.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Liebschner, D.
History
DepositionNov 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear factor of activated T-cells, cytoplasmic 2
B: Nuclear factor of activated T-cells, cytoplasmic 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8864
Polymers24,5522
Non-polymers3342
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-0 kcal/mol
Surface area11810 Å2
Unit cell
Length a, b, c (Å)48.775, 40.279, 57.419
Angle α, β, γ (deg.)90.000, 97.255, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 576 through 578 or resid 580...
d_2ens_1(chain "B" and (resid 576 through 578 or resid 580 through 653 or resid 655 through 677))

NCS domain segments:

Ens-ID: ens_1 / End auth comp-ID: PRO / End label comp-ID: PRO

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUAA576 - 5783 - 5
d_12VALVALAA580 - 6537 - 80
d_13LYSLYSAA655 - 67782 - 104
d_21GLUGLUBB576 - 5783 - 5
d_22VALVALBB580 - 6537 - 80
d_23LYSLYSBB655 - 67782 - 104

NCS oper: (Code: givenMatrix: (-0.574888471566, 0.386940764239, -0.720957758979), (-0.631580264377, -0.770029050331, 0.0903417472476), (-0.520201513752, 0.507279121014, 0.687064973982)Vector: 35. ...NCS oper: (Code: given
Matrix: (-0.574888471566, 0.386940764239, -0.720957758979), (-0.631580264377, -0.770029050331, 0.0903417472476), (-0.520201513752, 0.507279121014, 0.687064973982)
Vector: 35.2414630881, 15.5281686484, 8.09222003114)

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Components

#1: Protein Nuclear factor of activated T-cells, cytoplasmic 2 / NF-ATc2 / NFATc2 / NFAT pre-existing subunit / NF-ATp / T-cell transcription factor NFAT1


Mass: 12275.864 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2, NFAT1, NFATP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13469
#2: Chemical ChemComp-XS8 / (4~{S})-6-fluoranyl-3,4-dihydro-2~{H}-chromen-4-amine


Mass: 167.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10FNO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: containing 25% PEG 3350, 200 mM Sodium Chloride and 100 mM BIS-TRIS buffer at a pH of 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.547→56.96 Å / Num. obs: 24212 / % possible obs: 74.4 % / Redundancy: 2 % / Biso Wilson estimate: 17.76 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.33
Reflection shellResolution: 1.547→1.62 Å / CC1/2: 0.52

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Processing

Software
NameVersionClassification
PHENIXdev_4839refinement
PHENIXdev_4839refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P7H

1p7h


Resolution: 1.55→56.96 Å / SU ML: 0.1981 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.4617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 1183 4.89 %
Rwork0.1942 23029 -
obs0.1963 24212 74.4 %
all-48015 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.4 Å2
Refinement stepCycle: LAST / Resolution: 1.55→56.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 24 268 1974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271762
X-RAY DIFFRACTIONf_angle_d1.22742388
X-RAY DIFFRACTIONf_chiral_restr0.0759256
X-RAY DIFFRACTIONf_plane_restr0.0105311
X-RAY DIFFRACTIONf_dihedral_angle_d6.1013250
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.14481495239 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.620.3089140.289314X-RAY DIFFRACTION8.14
1.62-1.70.3142620.29041279X-RAY DIFFRACTION33.37
1.7-1.810.31911390.28782516X-RAY DIFFRACTION65.2
1.81-1.950.34321670.25833608X-RAY DIFFRACTION93.7
1.95-2.150.25742130.20993783X-RAY DIFFRACTION98.57
2.15-2.460.23681810.1883802X-RAY DIFFRACTION98.35
2.46-3.090.22392020.18483823X-RAY DIFFRACTION98.05
3.09-56.960.20542050.16833904X-RAY DIFFRACTION98.3
Refinement TLS params.Method: refined / Origin x: 14.0133951759 Å / Origin y: 7.29146038569 Å / Origin z: 13.5852543605 Å
111213212223313233
T0.121694625016 Å20.0169703077769 Å20.00267879759663 Å2-0.107370708487 Å2-0.000845034680906 Å2--0.0831573842863 Å2
L1.55954548873 °20.460464930381 °20.144407077586 °2-1.05420917525 °2-0.00586381720642 °2--0.274607620729 °2
S0.0160181758658 Å °-0.112075352526 Å °-0.00423377531153 Å °0.112729672309 Å °-0.0209710388501 Å °0.0094326031609 Å °0.0326344679542 Å °0.0239421065164 Å °0.00956202946223 Å °
Refinement TLS groupSelection details: all

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