+Open data
-Basic information
Entry | Database: PDB / ID: 3sg3 | ||||||
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Title | Crystal Structure of GCaMP3-D380Y | ||||||
Components | Myosin light chain kinase, Green fluorescent protein, Calmodulin-1 chimera | ||||||
Keywords | FLUORESCENT PROTEIN / calcium sensor | ||||||
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 kinase activity / 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 | Gallus gallus (chicken) Aequorea victoria (jellyfish) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Schreiter, E.R. / Akerboom, J. / Looger, L.L. | ||||||
Citation | Journal: J.Neurosci. / Year: 2012 Title: Optimization of a GCaMP calcium indicator for neural activity imaging. Authors: Akerboom, J. / Chen, T.W. / Wardill, T.J. / Tian, L. / Marvin, J.S. / Mutlu, S. / Calderon, N.C. / Esposti, F. / Borghuis, B.G. / Sun, X.R. / Gordus, A. / Orger, M.B. / Portugues, R. / ...Authors: Akerboom, J. / Chen, T.W. / Wardill, T.J. / Tian, L. / Marvin, J.S. / Mutlu, S. / Calderon, N.C. / Esposti, F. / Borghuis, B.G. / Sun, X.R. / Gordus, A. / Orger, M.B. / Portugues, R. / Engert, F. / Macklin, J.J. / Filosa, A. / Aggarwal, A. / Kerr, R.A. / Takagi, R. / Kracun, S. / Shigetomi, E. / Khakh, B.S. / Baier, H. / Lagnado, L. / Wang, S.S. / Bargmann, C.I. / Kimmel, B.E. / Jayaraman, V. / Svoboda, K. / Kim, D.S. / Schreiter, E.R. / Looger, L.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sg3.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sg3.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 3sg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sg3_validation.pdf.gz | 442.3 KB | Display | wwPDB validaton report |
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Full document | 3sg3_full_validation.pdf.gz | 448.7 KB | Display | |
Data in XML | 3sg3_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 3sg3_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/3sg3 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/3sg3 | HTTPS FTP |
-Related structure data
Related structure data | 3sg2C 3sg4C 3sg5C 3sg6C 3sg7C 3ek8S 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: 50749.668 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: D380Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Rattus norvegicus (Norway rat) Gene: GFP, Calm1, Calm, Cam, Cam1, CaMI / Production host: Escherichia coli (E. coli) References: UniProt: Q6LDG3, UniProt: P42212, UniProt: P0DP29, UniProt: P11799*PLUS | ||||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Sequence details | THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF ...THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M sodium chloride, 0.1 M Tris, pH 8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 20, 2009 / Details: Kohzu HLD-4 Double Crystal |
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 40392 / Num. obs: 40352 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rsym value: 0.132 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.612 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EK8 Resolution: 2.1→19.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.693 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: 29.175 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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