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Yorodumi- PDB-4gvd: Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gvd | ||||||
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Title | Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with Syndecan1 Peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / conformational change during phosphorylation / different binding pocket from phosphorylated sydencan1 / scaffold signaling protein for cell adhesion and cell junction / sydencan1 N-terminal Thr dansylation | ||||||
Function / homology | Function and homology information myoblast development / positive regulation of Schwann cell chemotaxis / striated muscle cell development / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS ...myoblast development / positive regulation of Schwann cell chemotaxis / striated muscle cell development / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / A tetrasaccharide linker sequence is required for GAG synthesis / extrinsic component of postsynaptic density membrane / HS-GAG biosynthesis / HS-GAG degradation / positive regulation of extracellular exosome assembly / Activated NTRK2 signals through CDK5 / Sertoli cell development / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cell-cell contact zone / positive regulation of exosomal secretion / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / cargo receptor activity / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / ureteric bud development / main axon / neuron projection extension / Syndecan interactions / small GTPase-mediated signal transduction / positive regulation of axonogenesis / Other interleukin signaling / NRAGE signals death through JNK / Rac protein signal transduction / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / canonical Wnt signaling pathway / positive regulation of epithelial to mesenchymal transition / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / Retinoid metabolism and transport / axonal growth cone / response to glucocorticoid / response to cAMP / RAC1 GTPase cycle / EPHB-mediated forward signaling / receptor-mediated endocytosis / lysosomal lumen / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / response to cocaine / Cell surface interactions at the vascular wall / response to hydrogen peroxide / receptor tyrosine kinase binding / response to toxic substance / ruffle membrane / kinase binding / Golgi lumen / response to calcium ion / G alpha (12/13) signalling events / cell-cell junction / cell migration / positive regulation of protein binding / microtubule binding / protein-containing complex assembly / microtubule / dendritic spine / Attachment and Entry / positive regulation of cell migration / external side of plasma membrane / neuronal cell body / glutamatergic synapse / lipid binding / synapse / positive regulation of cell population proliferation / cell surface / protein-containing complex / extracellular exosome / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Liu, X. / Shepherd, T.R. / Murray, A.M. / Xu, Z. / Fuentes, E.J. | ||||||
Citation | Journal: Structure / Year: 2013 Title: The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics. Authors: Liu, X. / Shepherd, T.R. / Murray, A.M. / Xu, Z. / Fuentes, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gvd.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gvd.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 4gvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/4gvd ftp://data.pdbj.org/pub/pdb/validation_reports/gv/4gvd | HTTPS FTP |
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-Related structure data
Related structure data | 4gvcC 3kzdS 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 10154.440 Da / Num. of mol.: 2 / Fragment: PDZ domain (UNP residues 841-930) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: human / Gene: TIAM1 / Plasmid: PET21A-6HIS-rTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13009 #2: Protein/peptide | Mass: 1016.081 Da / Num. of mol.: 2 / Fragment: UNP residues 303-310 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18827 |
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-Non-polymers , 4 types, 108 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | Q844H IS A NATURAL VARIANT. |
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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: 1.76 Å3/Da / Density % sol: 29.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1 M MES, 20% PEG8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 21, 2010 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50.946 Å / Num. all: 13299 / Num. obs: 13246 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.355 / 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 ENTRY 3KZD Resolution: 1.85→50.946 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.956 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 28.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50.946 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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