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Yorodumi- PDB-4zpv: Structure of MERS-Coronavirus Spike Receptor-binding Domain (Engl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zpv | ||||||
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Title | Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 2) | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Vaccine / Immunogen / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Human coronavirus EMC Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å | ||||||
Authors | Joyce, M.G. / Mascola, J.R. / Graham, B.S. / Kwong, P.D. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Evaluation of candidate vaccine approaches for MERS-CoV. Authors: Wang, L. / Shi, W. / Joyce, M.G. / Modjarrad, K. / Zhang, Y. / Leung, K. / Lees, C.R. / Zhou, T. / Yassine, H.M. / Kanekiyo, M. / Yang, Z.Y. / Chen, X. / Becker, M.M. / Freeman, M. / Vogel, ...Authors: Wang, L. / Shi, W. / Joyce, M.G. / Modjarrad, K. / Zhang, Y. / Leung, K. / Lees, C.R. / Zhou, T. / Yassine, H.M. / Kanekiyo, M. / Yang, Z.Y. / Chen, X. / Becker, M.M. / Freeman, M. / Vogel, L. / Johnson, J.C. / Olinger, G. / Todd, J.P. / Bagci, U. / Solomon, J. / Mollura, D.J. / Hensley, L. / Jahrling, P. / Denison, M.R. / Rao, S.S. / Subbarao, K. / Kwong, P.D. / Mascola, J.R. / Kong, W.P. / Graham, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zpv.cif.gz | 489.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zpv.ent.gz | 407.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/4zpv ftp://data.pdbj.org/pub/pdb/validation_reports/zp/4zpv | HTTPS FTP |
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-Related 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
#1: Antibody | Mass: 23118.822 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 23742.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #3: Protein | Mass: 22963.977 Da / Num. of mol.: 2 / Fragment: UNP residues 381-588 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus EMC (isolate United Kingdom/H123990006/2012) Strain: isolate United Kingdom/H123990006/2012 / Gene: S, 3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: K9N5Q8 #4: Sugar | |
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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: 2.5 Å3/Da / Density % sol: 50.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium cacodylate pH 6.5, 80 mM magnesium acetate, 14.5 % PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→43.547 Å / Num. obs: 19408 / % possible obs: 85.4 % / Redundancy: 5.2 % / Net I/σ(I): 32.4 |
Reflection shell | Resolution: 3.25→3.36 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2 / % possible all: 76.3 |
-Processing
Software |
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Refinement | Resolution: 3.2→43.547 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.06 / 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: 3.2→43.547 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -5.4659 Å / Origin y: 9.2014 Å / Origin z: -27.5177 Å
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Refinement TLS group | Selection details: all |