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Yorodumi- PDB-7crg: Beta-strand-mediated dimeric formation of the extended Ig-like do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7crg | ||||||
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Title | Beta-strand-mediated dimeric formation of the extended Ig-like domains of human lamin A/C | ||||||
Components | Prelamin-A/C | ||||||
Keywords | NUCLEAR PROTEIN / lamin A/C / Ig-like domain / dimer | ||||||
Function / homology | Function and homology information structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / DNA double-strand break attachment to nuclear envelope / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization ...structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / DNA double-strand break attachment to nuclear envelope / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / lamin filament / protein localization to nuclear envelope / nuclear lamina / XBP1(S) activates chaperone genes / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / nuclear migration / regulation of telomere maintenance / negative regulation of cardiac muscle hypertrophy in response to stress / muscle organ development / intermediate filament / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of release of cytochrome c from mitochondria / protein localization to nucleus / heterochromatin formation / regulation of cell migration / Meiotic synapsis / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / protein localization / structural constituent of cytoskeleton / nuclear matrix / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / nuclear envelope / site of double-strand break / cellular response to hypoxia / nuclear membrane / nuclear speck / negative regulation of cell population proliferation / positive regulation of gene expression / structural molecule activity / perinuclear region of cytoplasm / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ahn, J. / Ha, N.C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Beta-strand-mediated dimeric formation of the Ig-like domains of human lamin A/C and B1. Authors: Ahn, J. / Lee, J. / Jeong, S. / Kang, S.M. / Park, B.J. / Ha, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7crg.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7crg.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 7crg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7crg_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 7crg_full_validation.pdf.gz | 433 KB | Display | |
Data in XML | 7crg_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 7crg_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/7crg ftp://data.pdbj.org/pub/pdb/validation_reports/cr/7crg | HTTPS FTP |
-Related structure data
Related structure data | 7dtgC 1ifrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17050.943 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02545 #2: Water | ChemComp-HOH / | |
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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: 2.61 Å3/Da / Density % sol: 50.69 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium Chloride, 0.05 M HEPES pH 7.5, 35%(v/v) Pentaerythritol Propoxylate (5/4PO/OH) |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 47954 / % possible obs: 98.1 % / Redundancy: 24.5 % / CC1/2: 0.995 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 47954 / Rpim(I) all: 0.073 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IFR Resolution: 1.8→39.38 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.86 / Phase error: 19.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→39.38 Å
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Refine LS restraints |
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LS refinement shell |
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