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- PDB-8ow4: 2.75 angstrom crystal structure of human NFAT1 with bound DNA -

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Basic information

Entry
Database: PDB / ID: 8ow4
Title2.75 angstrom crystal structure of human NFAT1 with bound DNA
Components
  • DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3')
  • DNA (5'-D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3')
  • Nuclear factor of activated T-cells, cytoplasmic 2
KeywordsDNA BINDING PROTEIN / Transcription factor
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 / 14-3-3 protein binding / cellular response to calcium ion / FCERI mediated Ca+2 mobilization / 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 / transcription by RNA polymerase II / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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
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: 2.75 Å
AuthorsLopez-Sagaseta, J. / Erausquin, E. / Hernandez-Morales, S. / Urdiciain, A. / Lasarte, J.J. / Lozano, T.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-108989RB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2017-21683 Spain
CitationJournal: Not published
Title: 2.75 angstrom crystal structure of human NFAT1 with bound DNA
Authors: Lopez-Sagaseta, J. / Erausquin, E. / Hernandez-Morales, S. / Urdiciain, A. / Lasarte, J.J. / Lozano, T.
History
DepositionApr 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_abbrev / _citation.journal_id_CSD

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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
W: DNA (5'-D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3')
C: DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3')
G: DNA (5'-D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3')
H: DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3')
B: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)86,0936
Polymers86,0936
Non-polymers00
Water1629
1
A: Nuclear factor of activated T-cells, cytoplasmic 2
G: DNA (5'-D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3')
H: DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)43,0473
Polymers43,0473
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-17 kcal/mol
Surface area16900 Å2
MethodPISA
2
W: DNA (5'-D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3')
C: DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3')
B: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)43,0473
Polymers43,0473
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-16 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.497, 94.426, 129.449
Angle α, β, γ (deg.)90.000, 93.568, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROPROPROAA395 - 67015 - 290
211PROPROHISHISBF395 - 64915 - 269
322DTDTDGDGWB4001 - 40151 - 15
422DTDTDGDGGD4001 - 40151 - 15
533DADADCDCCC5001 - 50151 - 15
633DADADCDCHE5001 - 50151 - 15

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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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: 33870.547 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: DNA chain DNA (5'-D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3')


Mass: 4657.059 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3')


Mass: 4518.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.61 Å3/Da / Density % sol: 65.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M sodium cacodylate pH 6.0, 8% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979181 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2022
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979181 Å / Relative weight: 1
ReflectionResolution: 2.75→82.242 Å / Num. obs: 30970 / % possible obs: 97.3 % / Redundancy: 4.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.056 / Rrim(I) all: 0.088 / Χ2: 0.94 / Net I/σ(I): 10.5
Reflection shellResolution: 2.75→2.88 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4185 / CC1/2: 0.863 / Rpim(I) all: 0.427 / Rrim(I) all: 0.665 / Χ2: 0.99 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→82.242 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.283 / WRfactor Rwork: 0.226 / SU B: 32.272 / SU ML: 0.284 / Average fsc free: 0.9398 / Average fsc work: 0.9613 / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.327
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2728 1717 5.545 %RANDOM
Rwork0.2159 29249 --
all0.219 ---
obs-30966 97.228 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 84.321 Å2
Baniso -1Baniso -2Baniso -3
1-4.826 Å20 Å26.151 Å2
2---3.875 Å20 Å2
3----1.705 Å2
Refinement stepCycle: LAST / Resolution: 2.75→82.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4027 1218 0 9 5254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0115478
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164369
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.6917680
X-RAY DIFFRACTIONr_angle_other_deg0.4981.54610220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0335511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.1821031
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05310663
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.29110184
X-RAY DIFFRACTIONr_chiral_restr0.0990.2867
X-RAY DIFFRACTIONr_chiral_restr_other0.0090.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02973
X-RAY DIFFRACTIONr_nbd_refined0.1980.2853
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.24115
X-RAY DIFFRACTIONr_nbtor_refined0.190.22397
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.247
X-RAY DIFFRACTIONr_nbd_other0.4370.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2360.24
X-RAY DIFFRACTIONr_mcbond_it5.4996.0922074
X-RAY DIFFRACTIONr_mcbond_other5.4976.0922074
X-RAY DIFFRACTIONr_mcangle_it8.1299.0982575
X-RAY DIFFRACTIONr_mcangle_other8.1289.0982576
X-RAY DIFFRACTIONr_scbond_it5.9336.1233404
X-RAY DIFFRACTIONr_scbond_other5.9326.1233405
X-RAY DIFFRACTIONr_scangle_it8.3779.15105
X-RAY DIFFRACTIONr_scangle_other8.3769.15106
X-RAY DIFFRACTIONr_lrange_it10.83275.7486014
X-RAY DIFFRACTIONr_lrange_other10.83275.7496015
X-RAY DIFFRACTIONr_ncsr_local_group_10.1090.055851
X-RAY DIFFRACTIONr_ncsr_local_group_20.0810.051355
X-RAY DIFFRACTIONr_ncsr_local_group_30.0660.051255
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.10890.05009
12AX-RAY DIFFRACTIONLocal ncs0.10890.05009
23AX-RAY DIFFRACTIONLocal ncs0.080860.05009
24AX-RAY DIFFRACTIONLocal ncs0.080860.05009
35AX-RAY DIFFRACTIONLocal ncs0.065670.0501
36AX-RAY DIFFRACTIONLocal ncs0.065670.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.75-2.8210.3991510.39621660.39623220.8830.90499.78470.377
2.821-2.8990.3911370.34621580.34922970.9010.92799.91290.327
2.899-2.9830.3591280.29420760.29822070.9290.94899.86410.271
2.983-3.0740.3471170.26820490.27221680.9290.95499.90780.248
3.074-3.1750.305980.22719730.23120730.9430.96899.90350.215
3.175-3.2860.311090.21518990.21920160.9410.97199.60320.21
3.286-3.410.336860.22518670.2319590.9340.96999.69370.224
3.41-3.5490.238930.22417800.22518760.9660.97299.84010.223
3.549-3.7060.305930.22913350.23318300.9410.97178.03280.23
3.706-3.8870.2851160.21714570.22217190.9480.97391.50670.218
3.887-4.0970.258800.19412930.19716460.960.97883.41430.202
4.097-4.3450.245840.17814580.18215460.9650.98199.74130.187
4.345-4.6440.214850.17213880.17414770.9680.98299.72920.189
4.644-5.0140.2281080.16612490.17113590.9630.98399.85280.187
5.014-5.4910.261700.18911980.19312710.9580.97899.7640.211
5.491-6.1360.275640.20210770.20611420.9580.97699.91240.225
6.136-7.0780.276490.1989580.20210090.950.97599.80180.229
7.078-8.6530.22370.1998530.28610.9650.97599.88390.239
8.653-12.170.225390.1936300.1956730.9710.97699.40560.235
12.17-82.2420.39530.3363840.3373970.9760.89397.48110.42
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2529-0.69760.82340.4047-0.54971.69580.01430.45350.06470.0309-0.2534-0.0142-0.01730.31530.2390.33790.00230.06710.47850.08540.2314-10.049230.176713.8672
21.6161-0.50950.88995.8601-0.43410.5060.0450.2668-0.1178-0.11570.02150.11410.00890.1916-0.06650.242-0.00560.10410.26170.04790.287622.723223.452134.8849
31.22062.20820.39394.7292-0.06421.124-0.183-0.0007-0.1007-0.304-0.0482-0.4917-0.1261-0.16030.23120.19560.02520.04480.25740.0760.345525.881629.998835.4007
40.9668-0.68580.71450.643-0.68141.7712-0.0011-0.0029-0.11070.24350.08390.069-0.0301-0.5827-0.08280.48830.01480.09720.27120.00530.2418-27.606630.383628.3039
50.6274-1.0618-0.58481.97321.37641.4117-0.1646-0.02170.02140.21410.03740.0518-0.04920.01130.12710.27180.02090.07320.31930.02370.2926-30.711736.797729.3034
60.0894-0.01420.21290.0068-0.04670.6651-0.04920.0198-0.01930.0328-0.01520.0048-0.06450.04990.06440.4355-0.066-0.00750.2822-0.00720.27345.794723.62353.235
Refinement TLS groupSelection: ALL

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