[English] 日本語
Yorodumi- PDB-7njz: X-ray crystallography study of RoAb13 which binds to PIYDIN, a pa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7njz | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystallography study of RoAb13 which binds to PIYDIN, a part of the CCR5 N terminal domain | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / CCR5 Peptidomimetic | ||||||
Function / homology | Function and homology information chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / coreceptor activity / cell chemotaxis / calcium-mediated signaling / chemotaxis / calcium ion transport / MAPK cascade / virus receptor activity / cell-cell signaling / actin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cellular response to lipopolysaccharide / endosome / cell surface receptor signaling pathway / inflammatory response / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / cell surface / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Helliwell, J.R. / Chayen, N. / Saridakis, E. / Govada, L. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Iucrj / Year: 2021 Title: X-ray crystallographic studies of RoAb13 bound to PIYDIN, a part of the N-terminal domain of C-C chemokine receptor 5. Authors: Govada, L. / Saridakis, E. / Kassen, S.C. / Bin-Ramzi, A. / Morgan, R.M. / Chain, B. / Helliwell, J.R. / Chayen, N.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7njz.cif.gz | 118 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7njz.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 7njz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7njz_validation.pdf.gz | 322.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7njz_full_validation.pdf.gz | 332.3 KB | Display | |
Data in XML | 7njz_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 7njz_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/7njz ftp://data.pdbj.org/pub/pdb/validation_reports/nj/7njz | HTTPS FTP |
-Related structure data
Related structure data | 7nw3C 4s2sS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4912886 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 24063.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
---|---|
#2: Antibody | Mass: 24459.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Protein/peptide | Mass: 733.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51681 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68 % / Description: Bipyramidal. |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.85 M Ammonium sulfate / PH range: 5.0 - 6.0 Temp details: All experiments were incubated in a temperature controlled Incubator at 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→73.53 Å / Num. obs: 13940 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 121.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.2→3.5 Å / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2703 / CC1/2: 0.95 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4S2S Resolution: 3.2→73.52 Å / SU ML: 0.6142 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.1435 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 121.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→73.52 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|