[English] 日本語
Yorodumi- PDB-8apy: Crystal structure of the H12A variant of the KDEL receptor bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8apy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the H12A variant of the KDEL receptor bound to sybody | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / Trafficking receptor / synthetic binder / KDELR | ||||||
Function / homology | Function and homology information KDEL sequence binding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-coated vesicle membrane / ER retention sequence binding / protein retention in ER lumen / COPI-mediated anterograde transport / maintenance of protein localization in endoplasmic reticulum / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport ...KDEL sequence binding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-coated vesicle membrane / ER retention sequence binding / protein retention in ER lumen / COPI-mediated anterograde transport / maintenance of protein localization in endoplasmic reticulum / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Parker, J.L. / Smith, K. / Newstead, S. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of the H12A variant of the KDEL receptor bound to sybody Authors: Parker, J.L. / Smith, K. / Newstead, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8apy.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8apy.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 8apy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8apy_validation.pdf.gz | 668.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8apy_full_validation.pdf.gz | 679.6 KB | Display | |
Data in XML | 8apy_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 8apy_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/8apy ftp://data.pdbj.org/pub/pdb/validation_reports/ap/8apy | HTTPS FTP |
-Related structure data
Related structure data | 6i6jS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24409.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: KDELR2, RCJMB04_8l23 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: Q5ZKX9 |
---|---|
#2: Antibody | Mass: 13611.107 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
#3: Chemical | ChemComp-OLC / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 30% v/v PEG 400 0.1 M Tris pH 8.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→42.79 Å / Num. obs: 18726 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 56 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.094 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.34→2.4 Å / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1 / Num. unique obs: 1371 / CC1/2: 0.406 / Rpim(I) all: 1.218 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6i6j Resolution: 2.34→42.79 Å / SU ML: 0.4856 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.9822 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→42.79 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|