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Yorodumi- PDB-8s0m: Crystal structure of the HKU1 receptor binding domain in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8s0m | ||||||
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Title | Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01 | ||||||
Components |
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Keywords | VIRAL PROTEIN/RECEPTOR / coronavirus receptor / VIRAL PROTEIN / PROTEASE / NANOBODY / VIRAL PROTEIN-RECEPTOR complex | ||||||
Function / homology | Function and homology information transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / endocytosis involved in viral entry into host cell / viral translation / Induction of Cell-Cell Fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / endocytosis involved in viral entry into host cell / viral translation / Induction of Cell-Cell Fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Vicugna pacos (alpaca) Human coronavirus HKU1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å | ||||||
Authors | Duquerroy, S. / Fernandez, I. / Rey, F. | ||||||
Funding support | 1items
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Citation | Journal: Cell / Year: 2024 Title: Structural basis of TMPRSS2 zymogen activation and recognition by the HKU1 seasonal coronavirus. Authors: Fernandez, I. / Saunders, N. / Duquerroy, S. / Bolland, W.H. / Arbabian, A. / Baquero, E. / Blanc, C. / Lafaye, P. / Haouz, A. / Buchrieser, J. / Schwartz, O. / Rey, F.A. #1: Journal: Nature / Year: 2023 Title: TMPRSS2 is a functional receptor for human coronavirus HKU1 Authors: Saunders, N. / Fernandez, I. / Planchais, C. / Michel, V. / Rajah, M.M. / Baquero Salazar, E. / Postal, J. / Porrot, F. / Guivel-Benhassine, F. / Blanc, C. / Chauveau-Le Friec, G. / Martin, ...Authors: Saunders, N. / Fernandez, I. / Planchais, C. / Michel, V. / Rajah, M.M. / Baquero Salazar, E. / Postal, J. / Porrot, F. / Guivel-Benhassine, F. / Blanc, C. / Chauveau-Le Friec, G. / Martin, A. / Grzelak, L. / Oktavia, R.M. / Meola, A. / Ahouzi, O. / Hoover-Watson, H. / Prot, M. / Delaune, D. / Cornelissen, M. / Deijs, M. / Meriaux, V. / Mouquet, H. / Simon-Loriere, E. / van der Hoek, L. / Lafaye, P. / Rey, F. / Buchrieser, J. / Schwartz, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s0m.cif.gz | 666 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s0m.ent.gz | 556.1 KB | Display | PDB format |
PDBx/mmJSON format | 8s0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8s0m_validation.pdf.gz | 824.4 KB | Display | wwPDB validaton report |
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Full document | 8s0m_full_validation.pdf.gz | 842.8 KB | Display | |
Data in XML | 8s0m_validation.xml.gz | 56.7 KB | Display | |
Data in CIF | 8s0m_validation.cif.gz | 76.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/8s0m ftp://data.pdbj.org/pub/pdb/validation_reports/s0/8s0m | HTTPS FTP |
-Related structure data
Related structure data | 8s0lC 8s0nC C: citing same article (ref.) |
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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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules BEAD
#1: Protein | Mass: 43678.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) References: UniProt: O15393, transmembrane protease serine 2 #3: Protein | Mass: 40835.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus HKU1 (isolate N5) / Gene: S, 3 / Cell (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q0ZME7 |
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-Antibody , 1 types, 2 molecules UV
#2: Antibody | Mass: 14961.493 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) |
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-Sugars , 2 types, 5 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 3 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 6.22 Å3/Da / Density % sol: 80.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.35 M NaH2PO4, 0.65 M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 283 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 3.55→25 Å / Num. obs: 58457 / % possible obs: 99.6 % / Redundancy: 43.3 % / CC1/2: 1 / Rmerge(I) obs: 0.265 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 3.55→3.64 Å / Redundancy: 41.4 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4358 / CC1/2: 0.223 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.55→24.97 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.55→24.97 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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