+Open data
-Basic information
Entry | Database: PDB / ID: 7ur2 | ||||||||||||
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Title | Crystal structure of the Sec14 domain of the RhoGEF Kalirin | ||||||||||||
Components | Isoform 7 of Kalirin | ||||||||||||
Keywords | LIPID BINDING PROTEIN / Ras homologous guanine nucleotide exchange factor / CRAL-TRIO domain / spectrin repeat / lysophospholipids | ||||||||||||
Function / homology | Function and homology information EPHB-mediated forward signaling / maternal process involved in parturition / NRAGE signals death through JNK / RAC1 GTPase cycle / RHOA GTPase cycle / RHOG GTPase cycle / G alpha (q) signalling events / modification of postsynaptic actin cytoskeleton / G alpha (12/13) signalling events / regulation of dendrite development ...EPHB-mediated forward signaling / maternal process involved in parturition / NRAGE signals death through JNK / RAC1 GTPase cycle / RHOA GTPase cycle / RHOG GTPase cycle / G alpha (q) signalling events / modification of postsynaptic actin cytoskeleton / G alpha (12/13) signalling events / regulation of dendrite development / negative regulation of growth hormone secretion / MAPK6/MAPK4 signaling / regulation of modification of postsynaptic actin cytoskeleton / positive regulation of dendritic spine morphogenesis / habituation / maternal behavior / NMDA selective glutamate receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / extrinsic component of membrane / social behavior / lactation / adult locomotory behavior / axonogenesis / guanyl-nucleotide exchange factor activity / axon guidance / memory / presynapse / nervous system development / postsynaptic density / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / nucleoplasm / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å | ||||||||||||
Authors | Li, Y. / Doukov, T.I. / Hao, B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure of the Sec14 domain of Kalirin reveals a distinct class of lipid-binding module in RhoGEFs. Authors: Li, Y. / Pustovalova, Y. / Doukov, T.I. / Hoch, J.C. / Mains, R.E. / Eipper, B.A. / Hao, B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ur2.cif.gz | 569.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ur2.ent.gz | 473 KB | Display | PDB format |
PDBx/mmJSON format | 7ur2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ur2_validation.pdf.gz | 497.9 KB | Display | wwPDB validaton report |
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Full document | 7ur2_full_validation.pdf.gz | 507.2 KB | Display | |
Data in XML | 7ur2_validation.xml.gz | 63.1 KB | Display | |
Data in CIF | 7ur2_validation.cif.gz | 92.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/7ur2 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/7ur2 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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8 |
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Unit cell |
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-Components
#1: Protein | Mass: 21742.564 Da / Num. of mol.: 8 / Fragment: Sec14 domain (UNP residues 2-192) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kalrn / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A2CG49, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM sodium cacodylate, pH 6.5, 0.2 M ammonium sulfate, 20-25% PEG3350, 0.2 M sodium chloride |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.89→78.64 Å / Num. obs: 137673 / % possible obs: 95.9 % / Redundancy: 18.3 % / Biso Wilson estimate: 35.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.015 / Rrim(I) all: 0.063 / Net I/σ(I): 31.6 | |||||||||||||||||||||||||
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 19 % / Rmerge(I) obs: 1.294 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6729 / CC1/2: 0.907 / Rpim(I) all: 0.303 / Rrim(I) all: 1.329 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.89→61.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.124
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Displacement parameters | Biso max: 261.83 Å2 / Biso mean: 48.49 Å2 / Biso min: 17.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.89→61.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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