+Open data
-Basic information
Entry | Database: PDB / ID: 6ieb | ||||||
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Title | Structure of RVFV Gn and human monoclonal antibody R15 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/IMMUNE SYSTEM / RVFV / antibody / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information host cell mitochondrial outer membrane / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rift valley fever virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.409 Å | ||||||
Authors | Wang, Q.H. / Wu, Y. / Gao, F. / Qi, J.X. / Gao, G.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Microbiol / Year: 2019 Title: Neutralization mechanism of human monoclonal antibodies against Rift Valley fever virus. Authors: Wang, Q. / Ma, T. / Wu, Y. / Chen, Z. / Zeng, H. / Tong, Z. / Gao, F. / Qi, J. / Zhao, Z. / Chai, Y. / Yang, H. / Wong, G. / Bi, Y. / Wu, L. / Shi, R. / Yang, M. / Song, J. / Jiang, H. / An, ...Authors: Wang, Q. / Ma, T. / Wu, Y. / Chen, Z. / Zeng, H. / Tong, Z. / Gao, F. / Qi, J. / Zhao, Z. / Chai, Y. / Yang, H. / Wong, G. / Bi, Y. / Wu, L. / Shi, R. / Yang, M. / Song, J. / Jiang, H. / An, Z. / Wang, J. / Yilma, T.D. / Shi, Y. / Liu, W.J. / Liang, M. / Qin, C. / Gao, G.F. / Yan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ieb.cif.gz | 277.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ieb.ent.gz | 229 KB | Display | PDB format |
PDBx/mmJSON format | 6ieb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ieb_validation.pdf.gz | 471.1 KB | Display | wwPDB validaton report |
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Full document | 6ieb_full_validation.pdf.gz | 487.1 KB | Display | |
Data in XML | 6ieb_validation.xml.gz | 50.6 KB | Display | |
Data in CIF | 6ieb_validation.cif.gz | 71.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/6ieb ftp://data.pdbj.org/pub/pdb/validation_reports/ie/6ieb | 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
#1: Antibody | Mass: 23243.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 21914.367 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: Protein | Mass: 34940.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rift valley fever virus Production host: Insect cell expression vector pTIE1 (others) References: UniProt: H9BSP3, UniProt: P03518*PLUS #4: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 56.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PH6.5, 0.1M Amino acids, 0.1M Buffer System 1, 30.00% v/v P500MME/P20K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 64619 / % possible obs: 95.8 % / Redundancy: 3.2 % / CC1/2: 0.991 / Rpim(I) all: 0.051 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.1 / CC1/2: 0.628 / Rpim(I) all: 0.54 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Resolution: 2.409→38.56 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.409→38.56 Å
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Refine LS restraints |
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LS refinement shell |
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