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- PDB-1p7h: Structure of NFAT1 bound as a dimer to the HIV-1 LTR kB element -

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Basic information

Entry
Database: PDB / ID: 1p7h
TitleStructure of NFAT1 bound as a dimer to the HIV-1 LTR kB element
Components
  • 5'-D(*AP*AP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*A)-3'
  • 5'-D(*TP*TP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*A)-3'
  • Nuclear factor of activated T-cells, cytoplasmic 2NFAT
KeywordsTranscription/DNA / DNA Binding protein / Transcription regulation / Activator / 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: 2.6 Å
AuthorsGiffin, M.J. / Stroud, J.C. / Bates, D.L. / von Koenig, K.D. / Hardin, J. / Chen, L.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure of NFAT1 bound as a dimer to the HIV-1 LTR kappa B element
Authors: Giffin, M.J. / Stroud, J.C. / Bates, D.L. / von Koenig, K.D. / Hardin, J. / Chen, L.
History
DepositionMay 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: 5'-D(*AP*AP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*A)-3'
B: 5'-D(*TP*TP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*A)-3'
C: 5'-D(*AP*AP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*A)-3'
D: 5'-D(*TP*TP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*A)-3'
L: Nuclear factor of activated T-cells, cytoplasmic 2
M: Nuclear factor of activated T-cells, cytoplasmic 2
N: Nuclear factor of activated T-cells, cytoplasmic 2
O: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)148,3048
Polymers148,3048
Non-polymers00
Water3,405189
1
A: 5'-D(*AP*AP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*A)-3'
B: 5'-D(*TP*TP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*A)-3'
L: Nuclear factor of activated T-cells, cytoplasmic 2
M: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)74,1524
Polymers74,1524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*AP*AP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*A)-3'
D: 5'-D(*TP*TP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*A)-3'
N: Nuclear factor of activated T-cells, cytoplasmic 2
O: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)74,1524
Polymers74,1524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.107, 80.321, 80.308
Angle α, β, γ (deg.)71.20, 78.97, 78.94
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 4609.009 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*TP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*A)-3'


Mass: 4568.985 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
Nuclear factor of activated T-cells, cytoplasmic 2 / NFAT / T cell transcription factor NFAT1 / NFAT pre-existing subunit / NF-ATp


Mass: 32486.977 Da / Num. of mol.: 4 / Fragment: NFAT1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2 OR NFAT1 OR NFATP / References: UniProt: Q13469
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
22 mMspermine1drop
31 mMdithiothreitol1drop
4100 mM1dropNaCl
58 %(v/v)glycerol1drop
6350 mM1dropNH4OAc
750 mMTris-HCl1reservoirpH8.1
8100 mM1reservoirNaCl
914 %(w/v)PEG30001reservoir
102 mMspermine1reservoir
112 mMdithiothreitol1reservoir
1210 %(v/v)glycerol1reservoir

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Data collection

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: 2.5→29.68 Å / Num. all: 51229 / Num. obs: 51229 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 45.4 Å2
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / % possible obs: 93.9 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.68 Å / % possible obs: 58.6 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
Adxvdata processing
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 379385.01 / Data cutoff high rms absF: 379385.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4740 10.1 %RANDOM
Rwork0.231 ---
all0.265 51229 --
obs0.231 47083 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.7913 Å2 / ksol: 0.312537 e/Å3
Displacement parametersBiso mean: 56.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å2-4.72 Å2-4.63 Å2
2---1.63 Å23.39 Å2
3----0.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8988 1218 0 189 10395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.111.5
X-RAY DIFFRACTIONc_mcangle_it5.122
X-RAY DIFFRACTIONc_scbond_it3.972
X-RAY DIFFRACTIONc_scangle_it6.312.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 531 10.5 %
Rwork0.394 4530 -
obs--57.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0076
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.361 / Rfactor Rwork: 0.339

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