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Yorodumi- PDB-4qzv: Bat-derived coronavirus HKU4 uses MERS-CoV receptor human CD26 fo... -
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-Basic information
Entry | Database: PDB / ID: 4qzv | |||||||||
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Title | Bat-derived coronavirus HKU4 uses MERS-CoV receptor human CD26 for cell entry | |||||||||
Components |
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Keywords | HYDROLASE/VIRAL PROTEIN / 8-BLADED BETA-PROPELLER DOMAIN / ALPHA/BETA HYDROLASE DOMAIN / BLADES IV AND V / CD26 BETA-PROPELLER / HYDROLASE-VIRAL PROTEIN COMPLEX | |||||||||
Function / homology | Function and homology information glucagon processing / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / serine-type peptidase activity / T cell activation / endocytosis involved in viral entry into host cell / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / virus receptor activity / lamellipodium / protease binding / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / positive regulation of cell population proliferation / host cell plasma membrane / virion membrane / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Tylonycteris bat coronavirus HKU4 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.592 Å | |||||||||
Authors | Gao, F.G. / Wang, Q.H. / Qi, J.X. / Lu, G.W. | |||||||||
Citation | Journal: Cell Host Microbe / Year: 2014 Title: Bat Origins of MERS-CoV Supported by Bat Coronavirus HKU4 Usage of Human Receptor CD26. Authors: Wang, Q.H. / Qi, J.X. / Yuan, Y. / Xuan, Y. / Han, P. / Wan, Y. / Ji, W. / Li, Y. / Wu, Y. / Wang, J. / Iwamoto, A. / Woo, P.C. / Yuen, K.Y. / Yan, J. / Lu, G.W. / Gao, G.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qzv.cif.gz | 774.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qzv.ent.gz | 644.8 KB | Display | PDB format |
PDBx/mmJSON format | 4qzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/4qzv ftp://data.pdbj.org/pub/pdb/validation_reports/qz/4qzv | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 85291.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV #2: Protein | Mass: 27023.508 Da / Num. of mol.: 2 / Fragment: receptor binding domain (UNP RESIDUES 372-611) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tylonycteris bat coronavirus HKU4 / Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A3EX94 |
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-Sugars , 3 types, 13 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 476 molecules
#6: 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: 3.7 Å3/Da / Density % sol: 66.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M sodium citrate, pH 5.5, 15% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.592→50 Å / Num. all: 102311 / Num. obs: 102311 / % possible obs: 98.02 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.592→46.301 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.592→46.301 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Origin x: 180.8006 Å / Origin y: 251.3016 Å / Origin z: 41.2624 Å
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Refinement TLS group | Selection details: ALL |