+Open data
-Basic information
Entry | Database: PDB / ID: 7bsd | ||||||
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Title | Complex structure of 1G5.3 Fab bound to ZIKV NS1c | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / Zika virus / NS1 / antibody / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / molecular adaptor activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / centrosome / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Zika virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | ||||||
Authors | Song, H. / Qi, J. / Gao, F.G. | ||||||
Citation | Journal: Science / Year: 2021 Title: A broadly protective antibody that targets the flavivirus NS1 protein. Authors: Modhiran, N. / Song, H. / Liu, L. / Bletchly, C. / Brillault, L. / Amarilla, A.A. / Xu, X. / Qi, J. / Chai, Y. / Cheung, S.T.M. / Traves, R. / Setoh, Y.X. / Bibby, S. / Scott, C.A.P. / ...Authors: Modhiran, N. / Song, H. / Liu, L. / Bletchly, C. / Brillault, L. / Amarilla, A.A. / Xu, X. / Qi, J. / Chai, Y. / Cheung, S.T.M. / Traves, R. / Setoh, Y.X. / Bibby, S. / Scott, C.A.P. / Freney, M.E. / Newton, N.D. / Khromykh, A.A. / Chappell, K.J. / Muller, D.A. / Stacey, K.J. / Landsberg, M.J. / Shi, Y. / Gao, G.F. / Young, P.R. / Watterson, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bsd.cif.gz | 228.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bsd.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/7bsd ftp://data.pdbj.org/pub/pdb/validation_reports/bs/7bsd | HTTPS FTP |
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-Related structure data
Related structure data | 7bscC 5iy3S 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: Antibody | Mass: 24405.377 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human) #2: Antibody | Mass: 23772.482 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: 20766.514 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Strain: Mr 766 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: A0A024B7W1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase #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: 3.48 Å3/Da / Density % sol: 64.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 14% v/vPoly(acrylic acid-co-maleic acid) solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.03907 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2018 |
Diffraction measurement | Details: 1.00 degrees, 0.2 sec, detector distance 500.00 mm / Method: \w scans |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03907 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.124 / Number: 626111 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 63619 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.621 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 62455 / % possible all: 100 |
Cell measurement | Reflection used: 626111 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IY3 Resolution: 2.53→49.5 Å / SU ML: 0.3608 / Cross valid method: FREE R-VALUE / Phase error: 25.8119 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.53→49.5 Å
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Refine LS restraints |
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LS refinement shell |
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