+Open data
-Basic information
Entry | Database: PDB / ID: 1cm1 | ||||||
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Title | MOTIONS OF CALMODULIN-SINGLE-CONFORMER REFINEMENT | ||||||
Components |
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Keywords | COMPLEX (CALCIUM-BINDING/TRANSFERASE) / COMPLEX (CALCIUM-BINDING-TRANSFERASE) / EF-HAND CALCIUM-BINDING PROTEIN / COMPLEX (CALCIUM-BINDING-TRANSFERASE) complex | ||||||
Function / homology | Function and homology information regulation of synaptic vesicle docking / glutamatergic postsynaptic density / HSF1-dependent transactivation / RAF activation / regulation of store-operated calcium channel activity / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / regulation of high voltage-gated calcium channel activity / neurotransmitter receptor transport to plasma membrane ...regulation of synaptic vesicle docking / glutamatergic postsynaptic density / HSF1-dependent transactivation / RAF activation / regulation of store-operated calcium channel activity / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / regulation of high voltage-gated calcium channel activity / neurotransmitter receptor transport to plasma membrane / : / calcium- and calmodulin-dependent protein kinase complex / Interferon gamma signaling / : / regulation of neuron migration / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / dendritic spine development / calcium-dependent protein serine/threonine kinase activity / : / establishment of protein localization to mitochondrial membrane / Trafficking of AMPA receptors / type 3 metabotropic glutamate receptor binding / positive regulation of calcium ion transport / Ca2+ pathway / presynaptic cytosol / negative regulation of hydrolase activity / establishment of protein localization to membrane / postsynaptic neurotransmitter receptor diffusion trapping / postsynaptic specialization membrane / GTPase activating protein binding / RAF/MAP kinase cascade / NMDA selective glutamate receptor signaling pathway / dendrite morphogenesis / regulation of synaptic vesicle endocytosis / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic cytosol / negative regulation of high voltage-gated calcium channel activity / calcium/calmodulin-dependent protein kinase activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Ion homeostasis / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cardiac muscle cell apoptotic process / regulation of neuronal synaptic plasticity / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / 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 / Unblocking of NMDA receptors, glutamate binding and activation / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of protein localization to plasma membrane / positive regulation of DNA binding / glutamate receptor binding / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / potassium ion transmembrane transport / voltage-gated potassium channel complex / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / adenylate cyclase activator activity / ionotropic glutamate receptor signaling pathway / nitric-oxide synthase regulator activity / dendrite cytoplasm / regulation of heart rate / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / response to ischemia / angiotensin-activated signaling pathway / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / Schaffer collateral - CA1 synapse / spindle microtubule / cellular response to type II interferon / spindle pole / response to calcium ion / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wall, M.E. / Phillips Jr., G.N. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Authors: Wall, M.E. / Clarage, J.B. / Phillips Jr., G.N. #1: Journal: Science / Year: 1993 Title: Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A. #2: Journal: Science / Year: 1992 Title: Target Enzyme Recognition by Calmodulin: 2.4 A Structure of a Calmodulin-Peptide Complex Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cm1.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cm1.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 1cm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cm1_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 1cm1_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 1cm1_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1cm1_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/1cm1 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/1cm1 | HTTPS FTP |
-Related structure data
Related structure data | 1cm4C 1cdlS 1cdmS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16721.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Description: SIGMA LOT 54H9558 / Organ: BRAIN / References: UniProt: P02593, UniProt: P62157*PLUS | ||
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#2: Protein/peptide | Mass: 2886.528 Da / Num. of mol.: 1 / Fragment: CALMODULIN BINDING DOMAIN, RESIDUES 290 - 314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P11275, EC: 2.7.1.123 | ||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion - hanging drop - microseeding / pH: 5.2 Details: DIFFRACTION-QUALITY CRYSTALS WERE MICROSEEDED IN HANGING DROPS OVER 100 MM SODIUM ACETATE AT PH 5.2, WITH 20% POLY-ETHYLENE GLYCOL 6000 (PEG 6000), 10 MM CALCIUM CHLORIDE AND 0.02% SODIUM ...Details: DIFFRACTION-QUALITY CRYSTALS WERE MICROSEEDED IN HANGING DROPS OVER 100 MM SODIUM ACETATE AT PH 5.2, WITH 20% POLY-ETHYLENE GLYCOL 6000 (PEG 6000), 10 MM CALCIUM CHLORIDE AND 0.02% SODIUM AZIDE. STOCK SOLUTIONS OF 24 MG/ML BOVINE BRAIN CALMODULIN (SIGMA LOT 54H9558), 14 MG/ML CAMKII-ALPHA PEPTIDE, AND 30% PEG WERE MIXED INTO HANGING DROPS IN ABOUT A 4-2-1 RATIO., vapor diffusion - hanging drop - microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 302 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: May 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: SINGLE-CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→10 Å / Num. obs: 11522 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 22.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2→2.07 Å / Rsym value: 0.24 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1CDM AND 1CDL Resolution: 2→10 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUES 74 - 83, WHICH ARE NOT PRESENT IN PDB ENTRY 1CDM, WERE ADDED FOR THIS REFINEMENT. AN INITIAL GUESS WAS OBTAINED FROM THE COORDINATES OF PDB ENTRY 1CDL. THESE RESIDUES DO NOT SHOW ...Details: RESIDUES 74 - 83, WHICH ARE NOT PRESENT IN PDB ENTRY 1CDM, WERE ADDED FOR THIS REFINEMENT. AN INITIAL GUESS WAS OBTAINED FROM THE COORDINATES OF PDB ENTRY 1CDL. THESE RESIDUES DO NOT SHOW CONNECTED ELECTRON DENSITY AT A LEVEL OF 1SIGMA.
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Displacement parameters | Biso mean: 41.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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