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- PDB-5v90: Crystal structure of ERp29 D-domain in complex with the P-domain ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v90 | ||||||
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Title | Crystal structure of ERp29 D-domain in complex with the P-domain of calreticulin | ||||||
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![]() | CHAPERONE / protein binding / protein folding | ||||||
Function / homology | ![]() Calnexin/calreticulin cycle / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / 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 ...Calnexin/calreticulin cycle / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / 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 / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of meiotic nuclear division / complement component C1q complex binding / sequestering of calcium ion / response to glycoside / sarcoplasmic reticulum lumen / protein folding in endoplasmic reticulum / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / hormone binding / cardiac muscle cell differentiation / molecular sequestering activity / 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 / protein secretion / negative regulation of neuron differentiation / protein unfolding / smooth endoplasmic reticulum / negative regulation of protein secretion / positive regulation of cell cycle / ERAD pathway / positive regulation of substrate adhesion-dependent cell spreading / protein folding chaperone / positive regulation of phagocytosis / transport vesicle / 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 / intracellular protein transport / positive regulation of MAP kinase activity / 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 / melanosome / 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 / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / external side of plasma membrane / negative regulation of gene expression / 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 / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / protein homodimerization activity / DNA binding / RNA binding / extracellular space / zinc ion binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kozlov, G. / Munoz-Escobar, J. / Gehring, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mapping the ER Interactome: The P Domains of Calnexin and Calreticulin as Plurivalent Adapters for Foldases and Chaperones. Authors: Kozlov, G. / Munoz-Escobar, J. / Castro, K. / Gehring, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.2 KB | Display | ![]() |
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PDB format | ![]() | 72.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.9 KB | Display | ![]() |
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Full document | ![]() | 457.5 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v8zC ![]() 2qc7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11903.626 Da / Num. of mol.: 2 / Fragment: UNP residues 158-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 4665.040 Da / Num. of mol.: 2 / Fragment: UNP residues 238-273 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-GOL / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 64.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.0 M ammonium sulfate, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6307 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→50 Å / Num. obs: 6735 / % possible obs: 99.4 % / Redundancy: 9.7 % / Rsym value: 0.106 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 3.25→3.31 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 6.9 / Num. unique all: 632 / Num. unique obs: 368 / Rsym value: 0.494 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QC7 Resolution: 3.255→43.34 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.255→43.34 Å
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Refine LS restraints |
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LS refinement shell |
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