+Open data
-Basic information
Entry | Database: PDB / ID: 4yeq | |||||||||
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Title | L4b Domain of Human Laminin alpha-2 | |||||||||
Components | Laminin subunit alpha-2 | |||||||||
Keywords | SUGAR BINDING PROTEIN / carbohydrate binding fold / laminin / extracellular matrix / ephrin receptor | |||||||||
Function / homology | Function and homology information regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / Laminin interactions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / protein complex involved in cell-matrix adhesion / muscle organ development / MET activates PTK2 signaling / maintenance of blood-brain barrier ...regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / Laminin interactions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / protein complex involved in cell-matrix adhesion / muscle organ development / MET activates PTK2 signaling / maintenance of blood-brain barrier / positive regulation of muscle cell differentiation / regulation of embryonic development / positive regulation of cell adhesion / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / synaptic cleft / regulation of cell migration / axon guidance / neuromuscular junction / sarcolemma / collagen-containing extracellular matrix / dendritic spine / cell adhesion / signaling receptor binding / structural molecule activity / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Toot, M. / Gat, Y. / Fass, D. | |||||||||
Funding support | Israel, 2items
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Citation | Journal: Febs J. / Year: 2015 Title: Laminin L4 domain structure resembles adhesion modules in ephrin receptor and other transmembrane glycoproteins. Authors: Moran, T. / Gat, Y. / Fass, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yeq.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yeq.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/4yeq ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4yeq | HTTPS FTP |
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-Related structure data
Related structure data | 4yepSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23654.203 Da / Num. of mol.: 1 / Fragment: L4b Domain, UNP residues 1177-1379 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMA2, LAMM / Plasmid: pMal-c2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24043 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 6.25 Å3/Da / Density % sol: 80.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM sodium malonate, 100 mM MgCl2, 10% PEG 200, 100 mM Tris, pH 7.0 |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.2→22.9 Å / Num. obs: 10031 / % possible obs: 96.6 % / Redundancy: 9.6 % / Net I/σ(I): 15.9 | ||||||||||||||||||
Reflection shell | Resolution: 3.2→3.314 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1.8 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YEP Resolution: 3.2→22.899 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.02 / 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: 3.2→22.899 Å
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Refine LS restraints |
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LS refinement shell |
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