+Open data
-Basic information
Entry | Database: PDB / ID: 3pos | ||||||
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Title | Crystal structure of the globular domain of human calreticulin | ||||||
Components | Calreticulin | ||||||
Keywords | CHAPERONE / legume lectin fold / CNX/CRT family / multi-functional / Carbohydrate binding / Peptide Binding / multi-compartmental | ||||||
Function / homology | Function and homology information Calnexin/calreticulin cycle / cytolytic granule / Assembly of Viral Components at the Budding Site / cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus ...Calnexin/calreticulin cycle / cytolytic granule / Assembly of Viral Components at the Budding Site / cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus / intracellular glucocorticoid receptor signaling pathway / endoplasmic reticulum quality control compartment / sequestering of calcium ion / regulation of meiotic nuclear division / response to glycoside / sarcoplasmic reticulum lumen / protein folding in endoplasmic reticulum / hormone binding / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / cardiac muscle cell differentiation / molecular sequestering activity / Scavenging by Class A Receptors / protein maturation by protein folding / Scavenging by Class F Receptors / cortical actin cytoskeleton organization / nuclear androgen receptor binding / response to testosterone / cellular response to lithium ion / smooth endoplasmic reticulum / protein localization to nucleus / negative regulation of neuron differentiation / positive regulation of cell cycle / positive regulation of phagocytosis / : / positive regulation of substrate adhesion-dependent cell spreading / protein folding chaperone / endocytic vesicle lumen / protein export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of endothelial cell migration / acrosomal vesicle / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / intracellular calcium ion homeostasis / cellular response to virus / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / unfolded protein binding / cellular senescence / integrin binding / protein folding / response to estradiol / nuclear envelope / ER-Phagosome pathway / protein-folding chaperone binding / spermatogenesis / carbohydrate binding / collagen-containing extracellular matrix / regulation of apoptotic process / negative regulation of translation / protein stabilization / ribosome / response to xenobiotic stimulus / iron ion binding / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / mRNA binding / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / DNA binding / extracellular space / RNA binding / extracellular exosome / zinc ion binding / extracellular region / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Chouquet, A. / Paidassi, H. / Ling, W.-L. / Frachet, P. / Houen, G. / Arlaud, G.J. / Gaboriaud, C. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: X-ray structure of the human calreticulin globular domain reveals a Peptide-binding area and suggests a multi-molecular mechanism Authors: Chouquet, A. / Paidassi, H. / Ling, W.L. / Frachet, P. / Houen, G. / Arlaud, G.J. / Gaboriaud, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pos.cif.gz | 175.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pos.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 3pos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/3pos ftp://data.pdbj.org/pub/pdb/validation_reports/po/3pos | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30146.271 Da / Num. of mol.: 3 Fragment: Globular domain, UNP residues 18-204 and 302-368 linked with GSG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALR, CRTC / Plasmid: pHFX-CRT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P27797 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.39 % |
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Crystal grow | Temperature: 277.1 K / Method: vapor diffusion, hanging drop Details: 30% PEG 4000, 0.1M sodium acetate, 0.1M Tris, pH 8.5-9, VAPOR DIFFUSION, HANGING DROP, temperature 277.1K PH range: 8.5 - 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97925 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 88382 / Num. obs: 88382 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.81 |
Reflection shell | Resolution: 1.65→1.7 Å / Redundancy: 13 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6434 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.94 Å / Cor.coef. Fo:Fc: 0.9545 / Cor.coef. Fo:Fc free: 0.9386 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.171 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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