+Open data
-Basic information
Entry | Database: PDB / ID: 1cll | ||||||
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Title | CALMODULIN STRUCTURE REFINED AT 1.7 ANGSTROMS RESOLUTION | ||||||
Components | CALMODULIN | ||||||
Keywords | CALCIUM-BINDING PROTEIN | ||||||
Function / homology | Function and homology information : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / regulation of synaptic vesicle endocytosis / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / regulation of synaptic vesicle endocytosis / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / Synthesis of IP3 and IP4 in the cytosol / nitric-oxide synthase binding / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of protein autophosphorylation / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / positive regulation of nitric-oxide synthase activity / mitochondrial membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / synaptic vesicle membrane / spindle pole / cellular response to type II interferon / response to calcium ion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Chattopadhyaya, R. / Quiocho, F.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1992 Title: Calmodulin structure refined at 1.7 A resolution. Authors: Chattopadhyaya, R. / Meador, W.E. / Means, A.R. / Quiocho, F.A. #1: Journal: Science / Year: 1992 Title: Target Enzyme Recognition by Calmodulin: 2.4 Angstroms Structure of a Calmodulin-Peptide Complex Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A. #2: Journal: J.Mol.Biol. / Year: 1988 Title: Structure of Calmodulin Refined at 2.2 Angstroms Resolution Authors: Babu, Y.S. / Bugg, C.E. / Cook, W.J. | ||||||
History |
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Remark 700 | SHEET THE ANTI-PARALLEL BETA SHEETS ARE EXTREMELY SHORT IN THIS STRUCTURE. THERE IS ADDITIONAL ...SHEET THE ANTI-PARALLEL BETA SHEETS ARE EXTREMELY SHORT IN THIS STRUCTURE. THERE IS ADDITIONAL CONNECTIVITY VIA WATERS BETWEEN THE TWO STRANDS OF EACH SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cll.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cll.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/1cll ftp://data.pdbj.org/pub/pdb/validation_reports/cl/1cll | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Homo sapiens (human) / References: UniProt: P62158, UniProt: P0DP23*PLUS | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-EOH / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.89 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. all: 46091 / Num. obs: 15417 / Rmerge(I) obs: 0.329 / Biso Wilson estimate: 25 Å2 |
-Processing
Software |
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Refinement | Resolution: 1.7→10 Å / σ(F): 0.5 Details: CRYSTAL PACKING IS EXTENSIVELY STUDIED IN THE CHATTOPADHYAYA ET AL. PAPER ON CALMODULIN, AND FACILE CRYSTAL GROWTH ALONG THE Z-DIRECTION EXPLAINED. THE AUTHORS ALSO HAVE REPORTED IN DETAIL ...Details: CRYSTAL PACKING IS EXTENSIVELY STUDIED IN THE CHATTOPADHYAYA ET AL. PAPER ON CALMODULIN, AND FACILE CRYSTAL GROWTH ALONG THE Z-DIRECTION EXPLAINED. THE AUTHORS ALSO HAVE REPORTED IN DETAIL ABOUT THE HYDROGEN BONDING WITHIN VARIOUS STRUCTURAL ELEMENTS IN THAT PUBLICATION. HYDRATION IS ALSO DESCRIBED. THESE ARE AREAS WHICH WERE NOT DEALT WITH IN THE BABU ET AL. (1988) PUBLICATION.
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 14469 / σ(F): 0.5 / Rfactor obs: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |