+Open data
-Basic information
Entry | Database: PDB / ID: 3ekj | ||||||
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Title | Calcium-free GCaMP2 (calcium binding deficient mutant) | ||||||
Components | Myosin light chain kinase, Green fluorescent protein, Calmodulin chimera | ||||||
Keywords | FLUORESCENT PROTEIN / GECI / GCaMP2 / cpGFP / calmodulin / M13 peptide / apo GCaMP2 / calcium-free / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / muscle structure development / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / presynaptic cytosol / regulation of synaptic vesicle endocytosis / regulation of synaptic vesicle exocytosis ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / muscle structure development / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / presynaptic cytosol / regulation of synaptic vesicle endocytosis / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / postsynaptic cytosol / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / cleavage furrow / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / stress fiber / : / titin binding / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / response to calcium ion / Schaffer collateral - CA1 synapse / cellular response to type II interferon / G2/M transition of mitotic cell cycle / spindle pole / calcium-dependent protein binding / serine-type endopeptidase inhibitor activity / lamellipodium / myelin sheath / growth cone / transmembrane transporter binding / calmodulin binding / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / extracellular space / nucleoplasm / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | artificial gene (others) Aequorea victoria (jellyfish) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Akerboom, J. / Velez Rivera, J.D. / Looger, L.L. / Schreiter, E.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design Authors: Akerboom, J. / Rivera, J.D. / Guilbe, M.M. / Malave, E.C. / Hernandez, H.H. / Tian, L. / Hires, S.A. / Marvin, J.S. / Looger, L.L. / Schreiter, E.R. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2 Authors: M Rodriguez Guilbe, M. / Alfaro Malave, E.C. / Akerboom, J. / Marvin, J.S. / Looger, L.L. / Schreiter, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ekj.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ekj.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ekj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ekj_validation.pdf.gz | 411.5 KB | Display | wwPDB validaton report |
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Full document | 3ekj_full_validation.pdf.gz | 417.5 KB | Display | |
Data in XML | 3ekj_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 3ekj_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/3ekj ftp://data.pdbj.org/pub/pdb/validation_reports/ek/3ekj | HTTPS FTP |
-Related structure data
Related structure data | 3ek4C 3ek7SC 3ek8C 3ekhC C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 50482.492 Da / Num. of mol.: 1 Mutation: T329G, E334Q, D359G, E370Q, D396G, E407Q, D432G, E443Q Source method: isolated from a genetically manipulated source Details: disrupted calcium-sensing GFP analog; contains circular permuted EGFP, the M13 fragment of myosin light chain kinase, 8-fold mutated rat calmodulin and a 6xHis-tag from pRSETA. Calcium ...Details: disrupted calcium-sensing GFP analog; contains circular permuted EGFP, the M13 fragment of myosin light chain kinase, 8-fold mutated rat calmodulin and a 6xHis-tag from pRSETA. Calcium binding sites are mutated to lower the calcium-binding affinity. Source: (gene. exp.) artificial gene (others), (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Rattus norvegicus (Norway rat) Plasmid: pRSETA / Gene: GFP, Calm1, Calm, Cam, Cam1, CaMI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P42212, UniProt: P0DP29, UniProt: P11799*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUE SER65 HAS BEEN MUTATED TO GLY. RESIDUES GLY65, TYR66, AND GLY67 CONSTITUTE THE CHROMOPHORE ...RESIDUE SER65 HAS BEEN MUTATED TO GLY. RESIDUES GLY65, TYR66, AND GLY67 CONSTITUTE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 28, 2008 |
Radiation | Monochromator: Diamond(1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→31.94 Å / Num. obs: 10580 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.154 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.617 / % possible all: 98.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EK7 Resolution: 2.8→31.88 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.837 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.912 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 1.461 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 25.982 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→31.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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