+Open data
-Basic information
Entry | Database: PDB / ID: 6iec | ||||||
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Title | Structure of RVFV Gn and human monoclonal antibody R17 | ||||||
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 | Rift valley fever virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 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 | 6iec.cif.gz | 778 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iec.ent.gz | 679 KB | Display | PDB format |
PDBx/mmJSON format | 6iec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/6iec ftp://data.pdbj.org/pub/pdb/validation_reports/ie/6iec | 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 34940.828 Da / Num. of mol.: 4 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 #2: Antibody | Mass: 12611.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 11867.927 Da / Num. of mol.: 4 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: 3.92 Å3/Da / Density % sol: 68.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M ammonium sulfate, 0.1M Tris 7.5, 20% w/v PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 58821 / % possible obs: 97.2 % / Redundancy: 6.5 % / CC1/2: 0.986 / Rpim(I) all: 0.09 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2 / CC1/2: 0.81 / Rpim(I) all: 0.0302 |
-Processing
Software |
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Refinement | Resolution: 3.2→47.56 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→47.56 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: -136.1501 Å / Origin y: 358.7399 Å / Origin z: -50.157 Å
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Refinement TLS group | Selection details: all |