+Open data
-Basic information
Entry | Database: PDB / ID: 7e3m | ||||||
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Title | RORgamma LBD complexed with Panaxatriol and SRC2.2 | ||||||
Components |
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Keywords | IMMUNE SYSTEM/INHIBITOR / nuclear receptor / IMMUNE SYSTEM - inhibitor complex / IMMUNE SYSTEM-INHIBITOR complex | ||||||
Function / homology | Function and homology information cellular response to sterol / T-helper 17 cell differentiation / ligand-activated transcription factor activity / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...cellular response to sterol / T-helper 17 cell differentiation / ligand-activated transcription factor activity / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / adipose tissue development / lymph node development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Liu, Z.H. / Huang, J. / Lu, W.Q. / Tang, Y. / Wu, Z.R. | ||||||
Citation | Journal: To Be Published Title: Structure of human RORgammat LBD with SRC2.2 at 2.80 Angstroms resolution Authors: Liu, Z.H. / Huang, J. / Wu, Z.R. / Tang, Y. / Lu, W.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e3m.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e3m.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 7e3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e3m_validation.pdf.gz | 762.5 KB | Display | wwPDB validaton report |
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Full document | 7e3m_full_validation.pdf.gz | 762.8 KB | Display | |
Data in XML | 7e3m_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 7e3m_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/7e3m ftp://data.pdbj.org/pub/pdb/validation_reports/e3/7e3m | HTTPS FTP |
-Related structure data
Related structure data | 4xt9S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28307.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P51449 |
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#2: Protein/peptide | Mass: 1023.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-HVL / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.87 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 0.2M CaCl2 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979176 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 3, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979176 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 8384 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.013 / Rrim(I) all: 0.067 / Χ2: 0.943 / Net I/σ(I): 10.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XT9 Resolution: 2.8→39.94 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.868 / SU B: 12.712 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.27 Å2 / Biso mean: 34.691 Å2 / Biso min: 16.56 Å2
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Refinement step | Cycle: final / Resolution: 2.8→39.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.802→2.874 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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