+Open data
-Basic information
Entry | Database: PDB / ID: 4dx8 | ||||||
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Title | ICAP1 in complex with KRIT1 N-terminus | ||||||
Components |
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Keywords | PROTEIN BINDING / Protein-protein complex / PTB domain / Nudix fold / Protein-protein interaction / Membrane / nucleus | ||||||
Function / homology | Function and homology information negative regulation of protein targeting to membrane / regulation of integrin-mediated signaling pathway / negative regulation of cell adhesion involved in substrate-bound cell migration / biomineral tissue development / myoblast migration / negative regulation of substrate adhesion-dependent cell spreading / GTPase regulator activity / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endothelium development / negative regulation of focal adhesion assembly ...negative regulation of protein targeting to membrane / regulation of integrin-mediated signaling pathway / negative regulation of cell adhesion involved in substrate-bound cell migration / biomineral tissue development / myoblast migration / negative regulation of substrate adhesion-dependent cell spreading / GTPase regulator activity / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endothelium development / negative regulation of focal adhesion assembly / integrin activation / tube formation / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of fibroblast migration / cellular response to fibroblast growth factor stimulus / GDP-dissociation inhibitor activity / regulation of establishment of cell polarity / negative regulation of endothelial cell migration / small GTPase-mediated signal transduction / regulation of GTPase activity / positive regulation of Notch signaling pathway / receptor clustering / negative regulation of endothelial cell proliferation / positive regulation of focal adhesion assembly / regulation of cell adhesion mediated by integrin / positive regulation of cell division / centriolar satellite / positive regulation of protein targeting to membrane / cellular response to vascular endothelial growth factor stimulus / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / negative regulation of angiogenesis / positive regulation of stress fiber assembly / Notch signaling pathway / ruffle / phosphatidylinositol-4,5-bisphosphate binding / activation of protein kinase B activity / positive regulation of endothelial cell migration / blood vessel diameter maintenance / cell-matrix adhesion / cell redox homeostasis / negative regulation of protein binding / protein localization to plasma membrane / integrin-mediated signaling pathway / cell periphery / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / integrin binding / cell-cell junction / cell migration / lamellipodium / microtubule binding / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / cytoskeleton / nuclear body / intracellular signal transduction / negative regulation of cell population proliferation / positive regulation of cell population proliferation / protein kinase binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Liu, W. / Draheim, K. / Zhang, R. / Calderwood, D.A. / Boggon, T.J. | ||||||
Citation | Journal: Mol.Cell / Year: 2013 Title: Mechanism for KRIT1 Release of ICAP1-Mediated Suppression of Integrin Activation. Authors: Liu, W. / Draheim, K.M. / Zhang, R. / Calderwood, D.A. / Boggon, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dx8.cif.gz | 424 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dx8.ent.gz | 351.3 KB | Display | PDB format |
PDBx/mmJSON format | 4dx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dx8_validation.pdf.gz | 499.4 KB | Display | wwPDB validaton report |
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Full document | 4dx8_full_validation.pdf.gz | 521.2 KB | Display | |
Data in XML | 4dx8_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 4dx8_validation.cif.gz | 48.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/4dx8 ftp://data.pdbj.org/pub/pdb/validation_reports/dx/4dx8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 58 - 196 / Label seq-ID: 12 - 150
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-Components
#1: Protein | Mass: 16909.037 Da / Num. of mol.: 4 / Fragment: PTB domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: ICAP1, Integrin cytoplasmic domain-associated protein 1 (ICAP1), ITGB1BP1 Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14713 #2: Protein | Mass: 22911.543 Da / Num. of mol.: 4 / Fragment: Nudix domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: CCM1, Krev interaction trapped protein 1 (KRIT1), KRIT1 Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00522 #3: Chemical | ChemComp-BR / #4: 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: 2.9 Å3/Da / Density % sol: 57.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.06M AmSO4, 0.2M Ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2011 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→50 Å / Num. all: 61242 / Num. obs: 61242 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 85.4 Å2 / Rsym value: 0.087 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.54→2.64 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 6068 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.942 / SU ML: 0.182 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.244 / Stereochemistry target values: ML
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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 max: 283.36 Å2 / Biso mean: 102.7818 Å2 / Biso min: 52.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.54→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1038 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.54→2.602 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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