+
Open data
-
Basic information
Entry | Database: PDB / ID: 3pow | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the globular domain of human calreticulin | ||||||
![]() | calreticulin | ||||||
![]() | CHAPERONE / legume lectin fold / CNX/CRT family / multi-functional / Carbohydrate binding / Peptide Binding / multi-compartmental | ||||||
Function / homology | ![]() Calnexin/calreticulin cycle / cytolytic granule / positive regulation of dendritic cell chemotaxis / cortical granule / Assembly of Viral Components at the Budding Site / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / cellular response to electrical stimulus / endoplasmic reticulum quality control compartment ...Calnexin/calreticulin cycle / cytolytic granule / positive regulation of dendritic cell chemotaxis / cortical granule / Assembly of Viral Components at the Budding Site / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / cellular response to electrical stimulus / endoplasmic reticulum quality control compartment / complement component C1q complex binding / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of meiotic nuclear division / sequestering of calcium ion / response to glycoside / sarcoplasmic reticulum lumen / protein folding in endoplasmic reticulum / nuclear export signal receptor activity / hormone binding / negative regulation of intracellular steroid hormone receptor signaling pathway / molecular sequestering activity / cardiac muscle cell differentiation / protein maturation by protein folding / Scavenging by Class F Receptors / Scavenging by Class A Receptors / cortical actin cytoskeleton organization / nuclear androgen receptor binding / cellular response to lithium ion / response to testosterone / protein localization to nucleus / negative regulation of neuron differentiation / smooth endoplasmic reticulum / positive regulation of cell cycle / ERAD pathway / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / protein folding chaperone / endocytic vesicle lumen / protein export from nucleus / positive regulation of endothelial cell migration / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / cellular response to virus / intracellular calcium ion homeostasis / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / cellular senescence / unfolded protein binding / integrin binding / protein folding / response to estradiol / nuclear envelope / ER-Phagosome pathway / protein-folding chaperone binding / carbohydrate binding / spermatogenesis / regulation of apoptotic process / collagen-containing extracellular matrix / protein stabilization / negative regulation of translation / ribosome / response to xenobiotic stimulus / iron ion binding / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / ubiquitin protein ligase binding / calcium ion binding / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / DNA binding / RNA binding / extracellular space / zinc ion binding / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gaboriaud, C. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 121.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 90.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 418.8 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3posSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30146.271 Da / Num. of mol.: 1 Fragment: Globular domain, UNP residues 18-204 and 302-368 linked with GSG Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.49 % |
---|---|
Crystal grow | Temperature: 277.1 K / Method: vapor diffusion / pH: 6 Details: 30% PEG 4000, 0.2M ammonium acetate, 10mM magnesium acetate, and either 0.05M MES (pH 5.7 or 6.0), or 0.05M HEPES (pH 7.0), VAPOR DIFFUSION, temperature 277.1K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: horizontally side diffracting Silicon 111 crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 6705 / D res high: 1.54 Å / Num. obs: 6705 / % possible obs: 2.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→20 Å / Num. all: 39833 / Num. obs: 39833 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 20.093 Å2 / Rsym value: 0.07 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3POS Resolution: 1.55→10 Å / Cor.coef. Fo:Fc: 0.9472 / Cor.coef. Fo:Fc free: 0.9465 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.04 Å2 / Biso mean: 16.0774 Å2 / Biso min: 5.52 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.187 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 2.1858 Å / Origin y: 10.1515 Å / Origin z: 15.0518 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|