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Yorodumi- PDB-5zxv: Structural definition of a unique neutralization epitope on the r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zxv | ||||||
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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 / 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: 4.482 Å | ||||||
Authors | Zhang, S. / Wang, X. | ||||||
Funding support | China, 1items
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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 | 5zxv.cif.gz | 494.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zxv.ent.gz | 417.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zxv_validation.pdf.gz | 475.5 KB | Display | wwPDB validaton report |
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Full document | 5zxv_full_validation.pdf.gz | 510.3 KB | Display | |
Data in XML | 5zxv_validation.xml.gz | 47.5 KB | Display | |
Data in CIF | 5zxv_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/5zxv ftp://data.pdbj.org/pub/pdb/validation_reports/zx/5zxv | HTTPS FTP |
-Related structure data
Related structure data | 5yy5C 4l72S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 22929.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome coronavirus Production host: Insect cell expression vector pTIE1 (others) References: UniProt: K9N5Q8*PLUS #2: Antibody | Mass: 22745.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 22724.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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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: 3.13 Å3/Da / Density % sol: 60.76 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 2%(v/v) tacsimate pH 5.0, 0.1M sodium citrate tribasic dihydrate pH 5.6, 16%(w/v) polyethylene glycol 3,350 and 2M sodium thiocyanate |
-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: May 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 4.482→50 Å / Num. obs: 9351 / % possible obs: 96.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 4.5→4.6 Å / Redundancy: 3.1 % / Num. unique obs: 9351 / CC1/2: 0.541 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L72 Resolution: 4.482→35.438 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 52.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.482→35.438 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: -37.7227 Å / Origin y: 91.9355 Å / Origin z: -3.3713 Å
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Refinement TLS group | Selection details: all |