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- PDB-8r07: C-terminal Rel-homology Domain of NFAT1 -

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Basic information

Entry
Database: PDB / ID: 8r07
TitleC-terminal Rel-homology Domain of NFAT1
ComponentsNuclear factor of activated T-cells, cytoplasmic 2
KeywordsTRANSCRIPTION / NFAT1 / Transcription Factor
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 / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZak, K.M. / Boettcher, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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.
History
DepositionOct 30, 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

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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


Theoretical massNumber of molelcules
Total (without water)24,5522
Polymers24,5522
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint3 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.456, 40.320, 54.637
Angle α, β, γ (deg.)90.000, 90.235, 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 577 through 585 or resid 587...
d_2ens_1(chain "B" and (resid 577 through 585 or resid 587...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUTHRTHRAA577 - 5854 - 12
d_12SERSERSERSERAA58714
d_13LEULEUGLYGLYAA589 - 59316 - 20
d_14GLNGLNSERSERAA595 - 63322 - 60
d_15PROPROILEILEAA635 - 66162 - 88
d_16ARGARGVALVALAA665 - 67892 - 105
d_21LEULEUTHRTHRBB577 - 5854 - 12
d_22SERSERSERSERBB58714
d_23LEULEUGLYGLYBB589 - 59316 - 20
d_24GLNGLNSERSERBB595 - 63322 - 60
d_25PROPROILEILEBB635 - 66162 - 88
d_26ARGARGVALVALBB665 - 67892 - 105

NCS oper: (Code: givenMatrix: (-0.582125360166, 0.369001886019, -0.724546529331), (-0.605713251507, -0.791272010709, 0.0836663732846), (-0.542440339577, 0.487571751831, 0.684128836416)Vector: -20. ...NCS oper: (Code: given
Matrix: (-0.582125360166, 0.369001886019, -0.724546529331), (-0.605713251507, -0.791272010709, 0.0836663732846), (-0.542440339577, 0.487571751831, 0.684128836416)
Vector: -20.4088610185, -8.622282252, -10.0260749572)

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 25% PEG 3350, 200mM 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: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→36.18 Å / Num. obs: 19383 / % possible obs: 88.45 % / Redundancy: 2.8 % / Biso Wilson estimate: 11.89 Å2 / CC1/2: 1 / Net I/σ(I): 16.82
Reflection shellResolution: 1.74→1.83 Å / Num. unique obs: 1358 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIXdev_4839refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→36.18 Å / SU ML: 0.1491 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2979
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1839 978 5.05 %
Rwork0.1466 18405 -
obs0.1486 19383 88.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.93 Å2
Refinement stepCycle: LAST / Resolution: 1.74→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 0 266 1953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02391771
X-RAY DIFFRACTIONf_angle_d2.60452403
X-RAY DIFFRACTIONf_chiral_restr0.1308257
X-RAY DIFFRACTIONf_plane_restr0.0126319
X-RAY DIFFRACTIONf_dihedral_angle_d6.596232
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.56810133704 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.830.3032560.21411306X-RAY DIFFRACTION44.19
1.83-1.950.21121220.16292319X-RAY DIFFRACTION78.49
1.95-2.10.18331630.14422910X-RAY DIFFRACTION98.84
2.1-2.310.19461360.14172958X-RAY DIFFRACTION99.61
2.31-2.640.20131810.14622947X-RAY DIFFRACTION99.81
2.64-3.330.20581580.14312981X-RAY DIFFRACTION99.68
3.33-36.180.14481620.14152984X-RAY DIFFRACTION97.64
Refinement TLS params.Method: refined / Origin x: -9.68497862649 Å / Origin y: 0.678830115622 Å / Origin z: -14.1359203297 Å
111213212223313233
T0.100675420907 Å20.0156053586466 Å20.00609113522498 Å2-0.0869524468134 Å20.00428313673431 Å2--0.0731557753769 Å2
L1.23290580598 °20.175623578485 °20.164879531534 °2-0.614454136878 °2-0.00413336747549 °2--0.375154964538 °2
S0.0162086254879 Å °-0.0598378879233 Å °0.039224770153 Å °0.0281512025082 Å °-0.0076435006972 Å °0.0193150122509 Å °0.0330268985795 Å °-0.00797155541076 Å °-0.00282893720802 Å °
Refinement TLS groupSelection details: all

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