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- PDB-1s9k: Crystal Structure of Human NFAT1 and Fos-Jun on the IL-2 ARRE1 Site -

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Basic information

Entry
Database: PDB / ID: 1s9k
TitleCrystal Structure of Human NFAT1 and Fos-Jun on the IL-2 ARRE1 Site
Components
  • Human IL-2 ARRE1 Promoter Element, Minus Strand
  • Human IL-2 ARRE1 Promoter Element, Plus Strand
  • Nuclear factor of activated T-cells, cytoplasmic 2
  • Proto-oncogene protein c-fos
  • Transcription factor AP-1
KeywordsTRANSCRIPTION/DNA / Beta Barrel / Protein-DNA Complex / Double Helix / Ternary / Complex / B-ZIP / Basic Leucine Zipper / Coiled Coil / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


mononuclear cell differentiation / cellular response to prolactin / medium-term memory / lncRNA transcription / leading edge cell differentiation / cellular response to anisomycin / cAMP response element binding / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of DNA-templated transcription initiation ...mononuclear cell differentiation / cellular response to prolactin / medium-term memory / lncRNA transcription / leading edge cell differentiation / cellular response to anisomycin / cAMP response element binding / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of DNA-templated transcription initiation / integrated stress response signaling / cellular response to zinc ion starvation / release from viral latency / myotube cell development / skeletal muscle cell proliferation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / negative regulation of DNA binding / calcineurin-NFAT signaling cascade / WNT5:FZD7-mediated leishmania damping / neural retina development / cellular response to phorbol 13-acetate 12-myristate / SMAD protein signal transduction / conditioned taste aversion / NGF-stimulated transcription / positive regulation of osteoclast differentiation / host-mediated activation of viral transcription / cartilage development / response to steroid hormone / axon regeneration / cellular response to parathyroid hormone stimulus / positive regulation of myoblast fusion / response to corticosterone / CLEC7A (Dectin-1) induces NFAT activation / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / response to gravity / Activation of the AP-1 family of transcription factors / eyelid development in camera-type eye / response to immobilization stress / R-SMAD binding / outflow tract morphogenesis / response to light stimulus / ubiquitin-like protein ligase binding / myoblast proliferation / skeletal muscle cell differentiation / monocyte differentiation / positive regulation of epithelial cell migration / general transcription initiation factor binding / Calcineurin activates NFAT / host-mediated suppression of viral transcription / response to cAMP / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / phosphatase binding / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of vascular associated smooth muscle cell proliferation / JNK cascade / positive regulation of B cell proliferation / 14-3-3 protein binding / response to muscle stretch / NPAS4 regulates expression of target genes / positive regulation of endothelial cell proliferation / transcription repressor complex / FCERI mediated Ca+2 mobilization / transforming growth factor beta receptor signaling pathway / GTPase activator activity / cellular response to calcium ion / response to progesterone / osteoclast differentiation / response to endoplasmic reticulum stress / cellular response to epidermal growth factor stimulus / Regulation of PTEN gene transcription / response to activity / transcription coregulator binding / cellular response to reactive oxygen species / B cell receptor signaling pathway / FCERI mediated MAPK activation / TP53 Regulates Transcription of DNA Repair Genes / promoter-specific chromatin binding / microglial cell activation / liver development / female pregnancy / euchromatin / MAPK6/MAPK4 signaling / protein-DNA complex / response to insulin / cerebral cortex development / response to toxic substance / positive regulation of miRNA transcription / Pre-NOTCH Transcription and Translation / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / neuron differentiation / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / cellular response to tumor necrosis factor / Signaling by ALK fusions and activated point mutants / cell migration / regulation of cell population proliferation
Similarity search - Function
AP-1 transcription factor / Nuclear factor of activated T cells (NFAT) / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / Rel homology domain (RHD), DNA-binding domain / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain ...AP-1 transcription factor / Nuclear factor of activated T cells (NFAT) / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / Rel homology domain (RHD), DNA-binding domain / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / 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 / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein c-Fos / Transcription factor Jun / Nuclear factor of activated T-cells, cytoplasmic 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWang, D. / Stroud, J.C. / Chen, L.
CitationJournal: To be Published
Title: Crystal Structure of Human NFAT1 and Fos-Jun on the IL-2 ARRE1 Site
Authors: Wang, D. / Stroud, J.C. / Chen, L.
History
DepositionFeb 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Human IL-2 ARRE1 Promoter Element, Plus Strand
B: Human IL-2 ARRE1 Promoter Element, Minus Strand
C: Nuclear factor of activated T-cells, cytoplasmic 2
D: Proto-oncogene protein c-fos
E: Transcription factor AP-1


Theoretical massNumber of molelcules
Total (without water)56,6465
Polymers56,6465
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.769, 86.260, 84.044
Angle α, β, γ (deg.)90.00, 111.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain Human IL-2 ARRE1 Promoter Element, Plus Strand


Mass: 6211.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase synthesis
#2: DNA chain Human IL-2 ARRE1 Promoter Element, Minus Strand


Mass: 6050.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase synthesis
#3: Protein Nuclear factor of activated T-cells, cytoplasmic 2 / T cell transcription factor NFAT1 / NFAT pre-existing subunit / NF-ATp


Mass: 31874.303 Da / Num. of mol.: 1
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
#4: Protein Proto-oncogene protein c-fos / Cellular oncogene fos / G0/G1 switch regulatory protein 7


Mass: 6370.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOS, G0S7 / Production host: Escherichia coli (E. coli) / References: UniProt: P01100
#5: Protein Transcription factor AP-1 / Activator protein 1 / AP1 / Proto-oncogene c-jun / V-jun avian sarcoma virus 17 oncogene homolog / p39


Mass: 6139.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JUN / Production host: Escherichia coli (E. coli) / References: UniProt: P05412

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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: 3.86 Å3/Da / Density % sol: 68.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 300-400 mM Ammonium Acetate Salt, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Acetate Salt11
2H2O11
3Ammonium Acetate Salt12
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 16, 1996
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 16689 / Num. obs: 16172 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.2 Å / % possible all: 71.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2746 1443 Random
Rwork0.2423 --
all0.2423 15780 -
obs0.2423 14356 -
Solvent computationBsol: 18.2614 Å2 / ksol: 0.262883 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.522 Å20 Å2-1.978 Å2
2---19.397 Å20 Å2
3---8.875 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 814 0 0 3887
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it3.711.5
X-RAY DIFFRACTIONc_mcangle_it6.1552
X-RAY DIFFRACTIONc_scbond_it5.4882
X-RAY DIFFRACTIONc_scangle_it9.2032.5

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