+Open data
-Basic information
Entry | Database: PDB / ID: 4aqs | |||||||||
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Title | Laminin beta1 LN-LE1-4 structure | |||||||||
Components | LAMININ SUBUNIT BETA-1 | |||||||||
Keywords | CELL ADHESION | |||||||||
Function / homology | Function and homology information laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / basement membrane assembly / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway ...laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / basement membrane assembly / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / protein complex involved in cell-matrix adhesion / negative regulation of cell adhesion / odontogenesis / extracellular matrix structural constituent / positive regulation of muscle cell differentiation / positive regulation of cell adhesion / basement membrane / embryo implantation / substrate adhesion-dependent cell spreading / extracellular matrix / animal organ morphogenesis / neuron projection development / cell migration / integrin binding / collagen-containing extracellular matrix / learning or memory / positive regulation of cell migration / perinuclear region of cytoplasm / enzyme binding / extracellular space / extracellular region / nucleus Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.109 Å | |||||||||
Authors | Carafoli, F. / Hussain, S. / Hohenester, E. | |||||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystal Structures of the Network-Forming Short-Arm Tips of the Laminin Beta1 and Gamma1 Chains. Authors: Carafoli, F. / Hussain, S. / Hohenester, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aqs.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aqs.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 4aqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aqs_validation.pdf.gz | 743 KB | Display | wwPDB validaton report |
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Full document | 4aqs_full_validation.pdf.gz | 760.9 KB | Display | |
Data in XML | 4aqs_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 4aqs_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/4aqs ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aqs | HTTPS FTP |
-Related structure data
Related structure data | 4aqtC 1kloS 2y38S C: citing same article (ref.) 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: 58699.965 Da / Num. of mol.: 1 / Fragment: LN-LEA1-4 FRAGMENT, RESIDUES 22-542 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCEP-PU / Cell line (production host): HEK293 C18 / Production host: HOMO SAPIENS (human) / References: UniProt: P02469 |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.36 Å3/Da / Density % sol: 72 % / Description: NONE |
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Crystal grow | pH: 5 / Details: pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 18789 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 108.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.7 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2Y38 AND 1KLO Resolution: 3.109→76.475 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT / Bsol: 52.0014 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.8 Å2
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Refinement step | Cycle: LAST / Resolution: 3.109→76.475 Å
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Refine LS restraints |
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Xplor file |
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