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Yorodumi- PDB-5gmq: Structure of MERS-CoV RBD in complex with a fully human antibody MCA1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gmq | |||||||||
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Title | Structure of MERS-CoV RBD in complex with a fully human antibody MCA1 | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / 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 / membrane => GO:0016020 / 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 ...: / 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 / membrane => GO:0016020 / 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: 2.703 Å | |||||||||
Authors | Chen, C. / Wang, J.M. / Zou, T.T. / Gao, X.P. / Cui, S. / Jin, Q. | |||||||||
Citation | Journal: J. Infect. Dis. / Year: 2017 Title: Human Neutralizing Monoclonal Antibody Inhibition of Middle East Respiratory Syndrome Coronavirus Replication in the Common Marmoset. Authors: Chen, Z. / Bao, L. / Chen, C. / Zou, T. / Xue, Y. / Li, F. / Lv, Q. / Gu, S. / Gao, X. / Cui, S. / Wang, J. / Qin, C. / Jin, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gmq.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gmq.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/5gmq ftp://data.pdbj.org/pub/pdb/validation_reports/gm/5gmq | HTTPS FTP |
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-Related structure data
Related structure data | 5do2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules BC
#2: Antibody | Mass: 24475.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalian expression vector pCBio (others) |
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#3: Antibody | Mass: 23417.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalian expression vector pCBio (others) |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 25260.484 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 367-588 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: V5RDT9, UniProt: K9N5Q8*PLUS |
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#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 17 molecules
#5: Chemical | ChemComp-EDO / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.53 Å3/Da / Density % sol: 72.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.06 M Citric acid, 0.04 M Bis-tris propane, 16% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.703→40.33 Å / Num. obs: 36296 / % possible obs: 99.33 % / Redundancy: 6.8 % / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.703→3.17 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DO2 Resolution: 2.703→40.33 Å / SU ML: 0.44 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 31.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.703→40.33 Å
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Refine LS restraints |
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LS refinement shell |
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