+Open data
-Basic information
Entry | Database: PDB / ID: 8ahn | ||||||||||||
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Title | Sin Nombre virus Gn in complex with Fab SNV-42 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / Sin Nombre / virus / hantavirus / Fab / SNV-42 / complex | ||||||||||||
Function / homology | Function and homology information : / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / virion membrane / signal transduction / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Sin Nombre orthohantavirus Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Stass, R. / Bowden, T.A. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Nat Microbiol / Year: 2023 Title: Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody. Authors: Stass, R. / Engdahl, T.B. / Chapman, N.S. / Wolters, R.M. / Handal, L.S. / Diaz, S.M. / Crowe Jr., J.E. / Bowden, T.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ahn.cif.gz | 318 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ahn.ent.gz | 254.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ahn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ahn_validation.pdf.gz | 825.1 KB | Display | wwPDB validaton report |
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Full document | 8ahn_full_validation.pdf.gz | 832.1 KB | Display | |
Data in XML | 8ahn_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 8ahn_validation.cif.gz | 55.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/8ahn ftp://data.pdbj.org/pub/pdb/validation_reports/ah/8ahn | HTTPS FTP |
-Related structure data
Related structure data | 5opgS 5ur8S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 22906.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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#3: Antibody | Mass: 23642.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
-Protein / Non-polymers , 2 types, 762 molecules A
#1: Protein | Mass: 39286.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sin Nombre orthohantavirus / Production host: Homo sapiens (human) / References: UniProt: K9MNN9 |
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#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
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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: 2.99 Å3/Da / Density % sol: 58.86 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 0.2 M tri-ammonium citrate pH 7.0 and 20% w/v polyethylene glycol 3350 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2021 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.8→46.62 Å / Num. obs: 95210 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 24.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.033 / Rrim(I) all: 0.125 / Net I/σ(I): 13.4 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 14 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 5OPG and PDB ID 5UR8 Resolution: 1.8→46.62 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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