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Yorodumi- PDB-6kz5: Crystal Structure Analysis of the Csn-B-bounded NUR77 Ligand bind... -
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-Basic information
Entry | Database: PDB / ID: 6kz5 | ||||||
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Title | Crystal Structure Analysis of the Csn-B-bounded NUR77 Ligand binding Domain | ||||||
Components | Nuclear receptor subfamily 4 group A member 1 | ||||||
Keywords | TRANSCRIPTION / NR4A1 / Nur77 | ||||||
Function / homology | Function and homology information neurotransmitter secretion involved in regulation of skeletal muscle contraction / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis ...neurotransmitter secretion involved in regulation of skeletal muscle contraction / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / fat cell differentiation / skeletal muscle cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.45 Å | ||||||
Authors | Hong, W. / Chen, H. / Wu, Q. / Lin, T. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Blocking PPAR gamma interaction facilitates Nur77 interdiction of fatty acid uptake and suppresses breast cancer progression. Authors: Yang, P.B. / Hou, P.P. / Liu, F.Y. / Hong, W.B. / Chen, H.Z. / Sun, X.Y. / Li, P. / Zhang, Y. / Ju, C.Y. / Luo, L.J. / Wu, S.F. / Zhou, J.X. / Wang, Z.J. / He, J.P. / Li, L. / Zhao, T.J. / ...Authors: Yang, P.B. / Hou, P.P. / Liu, F.Y. / Hong, W.B. / Chen, H.Z. / Sun, X.Y. / Li, P. / Zhang, Y. / Ju, C.Y. / Luo, L.J. / Wu, S.F. / Zhou, J.X. / Wang, Z.J. / He, J.P. / Li, L. / Zhao, T.J. / Deng, X. / Lin, T. / Wu, Q. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Blocking PPAR gamma interaction facilitates Nur77 interdiction of fatty acid uptake and suppresses breast cancer progression Authors: Yang, P. / Hou, P. / Liu, F. / Hong, W. / Chen, H. / Sun, X. / Li, P. / Zhang, Y. / Ju, C. / Luo, L. / Wu, S. / Zhou, J. / Wang, Z. / He, J. / Li, L. / Zhao, T. / Deng, X. / Lin, T. / Wu, Q. #2: Journal: Nat. Chem. Biol. / Year: 2012 Title: The orphan nuclear receptor Nur77 regulates LKB1 localization and activates AMPK. Authors: Zhan, Y.Y. / Chen, Y. / Zhang, Q. / Zhuang, J.J. / Tian, M. / Chen, H.Z. / Zhang, L.R. / Zhang, H.K. / He, J.P. / Wang, W.J. / Wu, R. / Wang, Y. / Shi, C. / Yang, K. / Li, A.Z. / Xin, Y.Z. / ...Authors: Zhan, Y.Y. / Chen, Y. / Zhang, Q. / Zhuang, J.J. / Tian, M. / Chen, H.Z. / Zhang, L.R. / Zhang, H.K. / He, J.P. / Wang, W.J. / Wu, R. / Wang, Y. / Shi, C. / Yang, K. / Li, A.Z. / Xin, Y.Z. / Li, T.Y. / Yang, J.Y. / Zheng, Z.H. / Yu, C.D. / Lin, S.C. / Chang, C. / Huang, P.Q. / Lin, T. / Wu, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kz5.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kz5.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kz5_validation.pdf.gz | 662.6 KB | Display | wwPDB validaton report |
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Full document | 6kz5_full_validation.pdf.gz | 672.2 KB | Display | |
Data in XML | 6kz5_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 6kz5_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/6kz5 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/6kz5 | HTTPS FTP |
-Related structure data
Related structure data | 3v3eS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28745.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A1, GFRP1, HMR, NAK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22736 #2: Chemical | ChemComp-E4L / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.4 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: Crystals of apo-LBD was obtained at 4 degrees Celsius by hanging drop vapor diffusion. The droplets consisted of a 1:1 (v/v) mixture of LBD at 6 mg/ml, and the well solution consisted of 100 ...Details: Crystals of apo-LBD was obtained at 4 degrees Celsius by hanging drop vapor diffusion. The droplets consisted of a 1:1 (v/v) mixture of LBD at 6 mg/ml, and the well solution consisted of 100 mM sodium citrate (pH 4.6), 22% glycerol and 5% PEG4000. Crystals appeared after 24-48 h and were ready for data collection in 7 d. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: SDMS / Detector: PIXEL / Date: Oct 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 4.45→50 Å / Num. obs: 4038 / % possible obs: 91.2 % / Redundancy: 2.4 % / CC1/2: 0.914 / Rmerge(I) obs: 0.149 / Net I/σ(I): 4.514 |
Reflection shell | Resolution: 4.5→4.58 Å / Rmerge(I) obs: 0.492 / Num. unique obs: 197 / CC1/2: 0.656 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V3E Resolution: 4.45→33.28 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.745 / Cross valid method: THROUGHOUT / σ(F): 0 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.17 Å2 / Biso mean: 27.911 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 4.45→33.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.45→4.562 Å / Rfactor Rfree error: 0
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