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- PDB-7lsg: Crystal structure of the human neutralizing antibody Fab fragment... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lsg | ||||||
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Title | Crystal structure of the human neutralizing antibody Fab fragment T025 bound to TBEV EDIII (Siberian Subtype) | ||||||
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![]() | IMMUNE SYSTEM/VIRAL PROTEIN / Tick-borne encephalitis virus / antibody / EDIII / TBEV / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | ![]() flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Keeffe, J.R. / Bjorkman, P.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease. Authors: Agudelo, M. / Palus, M. / Keeffe, J.R. / Bianchini, F. / Svoboda, P. / Salat, J. / Peace, A. / Gazumyan, A. / Cipolla, M. / Kapoor, T. / Guidetti, F. / Yao, K.H. / Elsterova, J. / ...Authors: Agudelo, M. / Palus, M. / Keeffe, J.R. / Bianchini, F. / Svoboda, P. / Salat, J. / Peace, A. / Gazumyan, A. / Cipolla, M. / Kapoor, T. / Guidetti, F. / Yao, K.H. / Elsterova, J. / Teislerova, D. / Chrdle, A. / Honig, V. / Oliveira, T. / West, A.P. / Lee, Y.E. / Rice, C.M. / MacDonald, M.R. / Bjorkman, P.J. / Ruzek, D. / Robbiani, D.F. / Nussenzweig, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243 KB | Display | ![]() |
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PDB format | ![]() | 172 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 441.7 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lseC ![]() 7lsfC ![]() 4ogxS ![]() 6j5fS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 24834.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23424.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 10678.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: G8FGD9, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5% (+/-)-2-Methyl-2,4-pentanediol, 0.1M HEPES pH 7.5, 10% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.86→90.84 Å / Num. obs: 53401 / % possible obs: 95.8 % / Redundancy: 6 % / Biso Wilson estimate: 28.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.049 / Rrim(I) all: 0.123 / Net I/σ(I): 8.5 / Num. measured all: 320468 / Scaling rejects: 533 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OGX, 6J5F Resolution: 1.86→49.06 Å / SU ML: 0.2122 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2263 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: 34.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→49.06 Å
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Refine LS restraints |
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LS refinement shell |
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