+Open data
-Basic information
Entry | Database: PDB / ID: 1p7h | ||||||
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Title | Structure of NFAT1 bound as a dimer to the HIV-1 LTR kB element | ||||||
Components |
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Keywords | Transcription/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 / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Giffin, M.J. / Stroud, J.C. / Bates, D.L. / von Koenig, K.D. / Hardin, J. / Chen, L. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p7h.cif.gz | 269.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p7h.ent.gz | 212.8 KB | Display | PDB format |
PDBx/mmJSON format | 1p7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p7h_validation.pdf.gz | 479.1 KB | Display | wwPDB validaton report |
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Full document | 1p7h_full_validation.pdf.gz | 532.9 KB | Display | |
Data in XML | 1p7h_validation.xml.gz | 50.6 KB | Display | |
Data in CIF | 1p7h_validation.cif.gz | 69.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/1p7h ftp://data.pdbj.org/pub/pdb/validation_reports/p7/1p7h | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4609.009 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 4568.985 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 58.98 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.7913 Å2 / ksol: 0.312537 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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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
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LS refinement shell | *PLUS Rfactor Rfree: 0.361 / Rfactor Rwork: 0.339 |