+Open data
-Basic information
Entry | Database: PDB / ID: 2jd4 | ||||||
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Title | Mouse laminin alpha1 chain, domains LG4-5 | ||||||
Components | LAMININ SUBUNIT ALPHA-1 | ||||||
Keywords | METAL BINDING PROTEIN / LAMININ-111 / BASEMENT MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information laminin-3 complex / laminin complex / laminin-1 complex / retinal blood vessel morphogenesis / regulation of basement membrane organization / morphogenesis of an epithelial sheet / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / branching involved in salivary gland morphogenesis ...laminin-3 complex / laminin complex / laminin-1 complex / retinal blood vessel morphogenesis / regulation of basement membrane organization / morphogenesis of an epithelial sheet / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / branching involved in salivary gland morphogenesis / protein complex involved in cell-matrix adhesion / establishment of epithelial cell apical/basal polarity / camera-type eye development / blood vessel morphogenesis / extracellular matrix structural constituent / epithelial tube branching involved in lung morphogenesis / positive regulation of muscle cell differentiation / regulation of embryonic development / positive regulation of cell adhesion / basement membrane / regulation of cell migration / extracellular matrix / animal organ morphogenesis / axon guidance / neuron projection development / cell-cell junction / retina development in camera-type eye / collagen-containing extracellular matrix / cell surface receptor signaling pathway / cell adhesion / protein phosphorylation / signaling receptor binding / extracellular space / extracellular region / membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Harrison, D. / Hussain, S.A. / Combs, A.C. / Ervasti, J.M. / Yurchenco, P.D. / Hohenester, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structure and Cell Surface Anchorage Sites of Laminin {Alpha}1Lg4-5. Authors: Harrison, D. / Hussain, S.A. / Combs, A.C. / Ervasti, J.M. / Yurchenco, P.D. / Hohenester, E. #1: Journal: Embo J. / Year: 2000 Title: Structure of the C-Terminal Laminin G-Like Domain Pair of the Laminin Alpha2 Chain Harbouring Binding Sites for Alpha-Dystroglycan and Heparin Authors: Tisi, D. / Talts, J.F. / Timpl, R. / Hohenester, E. #2: Journal: Annu.Rev.Cell Dev.Biol. / Year: 2004 Title: Laminin Functions in Tissue Morphogenesis Authors: Miner, J.H. / Yurchenco, P.D. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jd4.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jd4.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 2jd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jd4_validation.pdf.gz | 440.2 KB | Display | wwPDB validaton report |
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Full document | 2jd4_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 2jd4_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 2jd4_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/2jd4 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/2jd4 | HTTPS FTP |
-Related structure data
Related structure data | 1dykS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41901.543 Da / Num. of mol.: 2 / Fragment: DOMAINS LG4-5, RESIDUES 2706-3084 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P19137 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 2738 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 2835 TO LYS ...ENGINEERED | Sequence details | VECTOR-DERIVED APLA SEQUENCE AT N-TERMINUS, GLYCOSYLATION SITES AND LONE CYSTEINE MUTATED ...VECTOR-DERIVED APLA SEQUENCE AT N-TERMINUS, GLYCOSYLAT | |
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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: 2.3 Å3/Da / Density % sol: 46.02 % |
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Crystal grow | pH: 8.5 / Details: pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 156499 / % possible obs: 97.3 % / Observed criterion σ(I): 4 / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DYK Resolution: 1.9→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.1583 Å2 / ksol: 0.334241 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.91 Å / Total num. of bins used: 50
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