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Open data
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Basic information
Entry | Database: PDB / ID: 3sg3 | ||||||
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Title | Crystal Structure of GCaMP3-D380Y | ||||||
![]() | Myosin light chain kinase, Green fluorescent protein, Calmodulin-1 chimera | ||||||
![]() | FLUORESCENT PROTEIN / calcium sensor | ||||||
Function / homology | ![]() 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 / regulation of synaptic vesicle endocytosis / organelle localization by membrane tethering / 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 / regulation of synaptic vesicle endocytosis / organelle localization by membrane tethering / regulation of synaptic vesicle exocytosis / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / protein phosphatase activator activity / cleavage furrow / adenylate cyclase binding / catalytic complex / calcium channel regulator activity / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / stress fiber / positive regulation of protein dephosphorylation / regulation of ryanodine-sensitive calcium-release channel activity / 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 / bioluminescence / regulation of cytokinesis / generation of precursor metabolites and energy / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / cellular response to type II interferon / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / lamellipodium / myelin sheath / growth cone / transmembrane transporter binding / calmodulin binding / protein kinase activity / protein domain specific binding / phosphorylation / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schreiter, E.R. / Akerboom, J. / Looger, L.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.9 KB | Display | ![]() |
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PDB format | ![]() | 77.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.3 KB | Display | ![]() |
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Full document | ![]() | 448.7 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sg2C ![]() 3sg4C ![]() 3sg5C ![]() 3sg6C ![]() 3sg7C ![]() 3ek8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() ![]() Gene: GFP, Calm1, Calm, Cam, Cam1, CaMI / Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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