+Open data
-Basic information
Entry | Database: PDB / ID: 3wld | ||||||
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Title | Crystal structure of monomeric GCaMP6m | ||||||
Components | Myosin light chain kinase, Green fluorescent protein, Calmodulin | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ding, J. / Luo, A.F. / Hu, L.Y. / Wang, D.C. / Shao, F. | ||||||
Citation | Journal: Sci China Life Sci / Year: 2014 Title: Structural basis of the ultrasensitive calcium indicator GCaMP6. Authors: Ding, J. / Luo, A.F. / Hu, L. / Wang, D. / Shao, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wld.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wld.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wld_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
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Full document | 3wld_full_validation.pdf.gz | 439.8 KB | Display | |
Data in XML | 3wld_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 3wld_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/3wld ftp://data.pdbj.org/pub/pdb/validation_reports/wl/3wld | HTTPS FTP |
-Related structure data
Related structure data | 3wlcC 3sg4S 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: 50398.176 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 37-55, 149-238, 2-144, 3-149 Mutation: M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, N61D, D79Y, M77G, K78S, T80R, S82T, R91G Source method: isolated from a genetically manipulated source Details: THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF UNP Q6LDG3, AN ENGINEERED LE LINKER, RESIDUES 149-239 OF UNP P42212, AN ENGINEERED ...Details: THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 OF UNP Q6LDG3, AN ENGINEERED LE LINKER, RESIDUES 149-239 OF UNP P42212, AN ENGINEERED GGTGGSMV LINKER, RESIDUES 2-144 OF UNP P42212, AN ENGINEERED LP LINKER, AND RESIDUES 3-149 OF UNP P0DP29. UNP P42212 RESIDUES S65, Y66, AND G67 ARE THE CHROMOPHORE CRO. Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Rattus norvegicus (Norway rat) Plasmid: pSUMO / Gene: GFP, Calm, Cam / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6LDG3, UniProt: P42212, UniProt: P0DP29, UniProt: P11799*PLUS | ||||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Sequence details | (1)THIS TRIPLE CHIMERA COMPRISES (FROM THE N-TERMINUS) AN ENGINEERED EXPRESSION TAG, RESIDUES 37-55 ...(1)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: 3.54 Å3/Da / Density % sol: 65.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1M HEPES, 18% w/v PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→60.44 Å / Num. all: 20398 / Num. obs: 20011 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2774 / Rsym value: 0.377 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SG4 Resolution: 2.7→54.059 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 20.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→54.059 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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