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Yorodumi- PDB-1a02: STRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN BOUND TO DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a02 | ||||||
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Title | STRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN BOUND TO DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / NFAT / NF-AT / AP-1 / FOS-JUN / QUATERNARY PROTEIN-DNA COMPLEX / TRANSCRIPTION SYNERGY / COMBINATORIAL GENE REGULATION / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information cAMP response element binding / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / myotube cell development / mononuclear cell differentiation / cellular response to prolactin / response to gravity ...cAMP response element binding / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / myotube cell development / mononuclear cell differentiation / cellular response to prolactin / response to gravity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / calcineurin-NFAT signaling cascade / negative regulation by host of viral transcription / skeletal muscle cell proliferation / cellular response to zinc ion starvation / cellular response to phorbol 13-acetate 12-myristate / WNT5:FZD7-mediated leishmania damping / conditioned taste aversion / SMAD protein signal transduction / NGF-stimulated transcription / positive regulation of osteoclast differentiation / R-SMAD binding / positive regulation by host of viral transcription / cartilage development / cellular response to parathyroid hormone stimulus / myoblast proliferation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / CLEC7A (Dectin-1) induces NFAT activation / positive regulation of myoblast fusion / nuclear chromosome / response to corticosterone / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of DNA binding / Activation of the AP-1 family of transcription factors / skeletal muscle cell differentiation / ubiquitin-like protein ligase binding / Calcineurin activates NFAT / general transcription initiation factor binding / cellular response to epidermal growth factor stimulus / response to immobilization stress / cellular response to cadmium ion / response to light stimulus / RNA polymerase II core promoter sequence-specific DNA binding / phosphatase binding / positive regulation of B cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / 14-3-3 protein binding / Regulation of PTEN gene transcription / response to cAMP / response to muscle stretch / cellular response to calcium ion / transcription coregulator binding / NPAS4 regulates expression of target genes / response to endoplasmic reticulum stress / FCERI mediated Ca+2 mobilization / GTPase activator activity / transforming growth factor beta receptor signaling pathway / osteoclast differentiation / positive regulation of miRNA transcription / response to activity / response to progesterone / female pregnancy / protein-DNA complex / TP53 Regulates Transcription of DNA Repair Genes / FCERI mediated MAPK activation / B cell receptor signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to reactive oxygen species / MAPK6/MAPK4 signaling / response to insulin / euchromatin / response to toxic substance / RNA polymerase II transcription regulator complex / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / Signaling by ALK fusions and activated point mutants / cell migration / Senescence-Associated Secretory Phenotype (SASP) / cellular response to tumor necrosis factor / cellular response to hypoxia / nervous system development / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Oxidative Stress Induced Senescence / Interleukin-4 and Interleukin-13 signaling / response to ethanol / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / transcription by RNA polymerase II / response to lipopolysaccharide / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / ribonucleoprotein complex / response to xenobiotic stimulus / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR/MAD / Resolution: 2.7 Å | ||||||
Authors | Chen, L. / Glover, J.N.M. / Hogan, P.G. / Rao, A. / Harrison, S.C. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA. Authors: Chen, L. / Glover, J.N. / Hogan, P.G. / Rao, A. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a02.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a02.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a02_validation.pdf.gz | 455.8 KB | Display | wwPDB validaton report |
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Full document | 1a02_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 1a02_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 1a02_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a02 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a02 | 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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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules AB
#1: DNA chain | Mass: 6178.024 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6084.993 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-AP-1 FRAGMENT ... , 2 types, 2 molecules FJ
#4: Protein | Mass: 6727.733 Da / Num. of mol.: 1 / Fragment: FOS / Mutation: C154S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01100 |
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#5: Protein | Mass: 6583.826 Da / Num. of mol.: 1 / Fragment: JUN / Mutation: C279S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05412 |
-Protein / Non-polymers , 2 types, 89 molecules N
#3: Protein | Mass: 34270.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: T-LYMPHOCYTE / Gene: NFAT1 / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q13469 |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: THE COMPLEX WAS CRYSTALLIZED IN 300-400 MM AMMONIUM ACETATE SALT, PH 7.5 (10 MM)., VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 16, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 22079 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 61 Å2 / Rsym value: 0.08 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.7 % / Rsym value: 0.43 / % possible all: 93.3 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % possible obs: 98.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Biso Wilson estimate: 61 Å2 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 93.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR/MAD / Resolution: 2.7→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUES N 478 - N 485 AND N 628 - N 634 ARE DISORDERED
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Displacement parameters | Biso mean: 51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 7.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.369 |