+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 response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / regulation of neuron migration / 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 / negative regulation of hydrolase activity / establishment of protein localization to membrane / postsynaptic neurotransmitter receptor diffusion trapping / presynaptic cytosol / GTPase activating protein binding / RAF/MAP kinase cascade / dendrite morphogenesis / postsynaptic specialization membrane / NMDA selective glutamate receptor signaling pathway / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of synaptic vesicle endocytosis / calcium/calmodulin-dependent protein kinase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / postsynaptic cytosol / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Ion homeostasis / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cardiac muscle cell apoptotic process / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / regulation of neuronal synaptic plasticity / : / 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 / Unblocking of NMDA receptors, glutamate binding and activation / regulation of protein localization to plasma membrane / calcium channel inhibitor activity / glutamate receptor binding / phosphatidylinositol 3-kinase binding / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / response to ischemia / angiotensin-activated signaling pathway / spindle microtubule / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / response to calcium ion / Schaffer collateral - CA1 synapse / G1/S transition of mitotic cell cycle / cellular response to type II interferon / G2/M transition of mitotic cell cycle / spindle pole 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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