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- PDB-5hzk: Crystal structure of photoinhibitable Intersectin1 containing wil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hzk | ||||||
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Title | Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in complex with Cdc42 | ||||||
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![]() | SIGNALING PROTEIN / Photoswitch / Chimera / Complex | ||||||
Function / homology | ![]() clathrin-dependent synaptic vesicle endocytosis / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis ...clathrin-dependent synaptic vesicle endocytosis / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / modulation by host of viral process / GTP-dependent protein binding / blue light photoreceptor activity / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / cardiac conduction system development / Inactivation of CDC42 and RAC1 / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / proline-rich region binding / regulation of lamellipodium assembly / nuclear migration / adherens junction organization / regulation of small GTPase mediated signal transduction / sprouting angiogenesis / DCC mediated attractive signaling / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / endosomal transport / regulation of mitotic nuclear division / RHOV GTPase cycle / establishment or maintenance of cell polarity / positive regulation of Rho protein signal transduction / phagocytosis, engulfment / intracellular vesicle / heart contraction / NRAGE signals death through JNK / Myogenesis / RHOJ GTPase cycle / exocytosis / RHOQ GTPase cycle / positive regulation of cytokinesis / Golgi organization / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / clathrin-coated pit / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / phagocytic vesicle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / positive regulation of DNA replication / secretory granule / filopodium / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / actin filament organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tarnawski, M. / Dagliyan, O. / Chu, P.H. / Shirvanyants, D. / Dokholyan, N.V. / Hahn, K.M. / Schlichting, I. | ||||||
![]() | ![]() Title: Engineering extrinsic disorder to control protein activity in living cells. Authors: Dagliyan, O. / Tarnawski, M. / Chu, P.H. / Shirvanyants, D. / Schlichting, I. / Dokholyan, N.V. / Hahn, K.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 539.3 KB | Display | ![]() |
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PDB format | ![]() | 447.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 45.3 KB | Display | |
Data in CIF | ![]() | 59.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hzhC ![]() 5hziC ![]() 5hzjC ![]() 1ki1S ![]() 2wkqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 21083.172 Da / Num. of mol.: 2 / Mutation: C188S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 58281.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: ITSN1, ITSN, SH3D1A, NPH1-1 / Production host: ![]() ![]() #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.1 M MES, 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 27085 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KI1, 2WKQ Resolution: 3.3→47.378 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→47.378 Å
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Refine LS restraints |
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LS refinement shell |
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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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