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Yorodumi- PDB-5yy5: Structural definition of a unique neutralization epitope on the r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yy5 | ||||||
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Title | Structural definition of a unique neutralization epitope on the receptor-binding domain of MERS-CoV spike glycoprotein | ||||||
Components |
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Keywords | VIRAL PROTEIN / MERS-CoV / spike glycorptotein / neutralizing antibody | ||||||
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 | Middle East respiratory syndrome coronavirus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Zhang, S. / Wang, P. / Zhou, P. / Wang, X. / Zhang, L. | ||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Structural Definition of a Unique Neutralization Epitope on the Receptor-Binding Domain of MERS-CoV Spike Glycoprotein Authors: Zhang, S. / Zhou, P. / Wang, P. / Li, Y. / Jiang, L. / Jia, W. / Wang, H. / Fan, A. / Wang, D. / Shi, X. / Fang, X. / Hammel, M. / Wang, S. / Wang, X. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yy5.cif.gz | 336.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yy5.ent.gz | 282.2 KB | Display | PDB format |
PDBx/mmJSON format | 5yy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yy5_validation.pdf.gz | 494.2 KB | Display | wwPDB validaton report |
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Full document | 5yy5_full_validation.pdf.gz | 513.5 KB | Display | |
Data in XML | 5yy5_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 5yy5_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/5yy5 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/5yy5 | HTTPS FTP |
-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
-Antibody , 4 types, 4 molecules HLCD
#2: Antibody | Mass: 12474.881 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 11720.712 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Antibody | Mass: 12216.610 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#5: Antibody | Mass: 11039.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 22987.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome coronavirus Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: K9N5Q8*PLUS #6: 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: 3.5 Å3/Da / Density % sol: 64.9 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / pH: 7 Details: tris pH7.5, polyethylene glycol 8000, ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 31541 / % possible obs: 99.2 % / Redundancy: 5.5 % / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.8→2.88 Å / Num. unique obs: 31541 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.51 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 40.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→41.51 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: 4.1861 Å / Origin y: 42.723 Å / Origin z: -102.7992 Å
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Refinement TLS group | Selection details: all |