+Open data
-Basic information
Entry | Database: PDB / ID: 8wku | ||||||
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Title | Complex structure of MjHKU4r-CoV-1 spike RBD bound to human CD26 | ||||||
Components |
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Keywords | VIRAL PROTEIN/HYDROLASE / MjHKU4r-CoV-1 / spike RBD / human CD26 / VIRAL PROTEIN-HYDROLASE complex | ||||||
Function / homology | Function and homology information glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / T cell activation / serine-type peptidase activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / virus receptor activity / lamellipodium / protease binding / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / apical plasma membrane / symbiont entry into host cell / membrane raft / serine-type endopeptidase activity / lysosomal membrane / focal adhesion / signaling receptor binding / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Manis javanica (Malayan pangolin) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Zhao, Z.N. / Chai, Y. / Gao, F. | ||||||
Funding support | China, 1items
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Citation | Journal: Embo Rep. / Year: 2024 Title: Molecular basis for receptor recognition and broad host tropism for merbecovirus MjHKU4r-CoV-1. Authors: Zhao, Z. / Li, X. / Chai, Y. / Liu, Z. / Wang, Q. / 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 | 8wku.cif.gz | 233.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wku.ent.gz | 169.2 KB | Display | PDB format |
PDBx/mmJSON format | 8wku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wku_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8wku_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8wku_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 8wku_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/8wku ftp://data.pdbj.org/pub/pdb/validation_reports/wk/8wku | HTTPS FTP |
-Related structure data
Related structure data | 4qzvS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 85291.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Production host: Homo sapiens (human) / References: UniProt: P27487 |
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#2: Protein | Mass: 27251.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Manis javanica HKU4-related coronavirus / Source: (gene. exp.) Manis javanica (Malayan pangolin) / Production host: Spodoptera frugiperda (fall armyworm) |
-Sugars , 7 types, 10 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||
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#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Sugar | |
-Details
Has ligand of interest | Y |
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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: 5.12 Å3/Da / Density % sol: 75.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Amino acids, 0.1 M buffer system 3 (Tris base; Bicine) and 30% v/v EDO_P8K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 22, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 54034 / % possible obs: 95.9 % / Redundancy: 7 % / CC1/2: 0.995 / Net I/σ(I): 10.31 |
Reflection shell | Resolution: 3.5→3.71 Å / Num. unique obs: 6746 / CC1/2: 0.625 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QZV Resolution: 3.5→45.78 Å / Cross valid method: FREE R-VALUE / σ(F): 268.92 / Phase error: 25.1102 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 107.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→45.78 Å
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Refine LS restraints |
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LS refinement shell |
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