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Yorodumi- PDB-7qqb: Crystal structure of the envelope glycoprotein complex of Puumala... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qqb | ||||||
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Title | Crystal structure of the envelope glycoprotein complex of Puumala virus in complex with the scFv fragment of the broadly neutralizing human antibody ADI-42898 | ||||||
Components |
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Keywords | VIRAL PROTEIN / hantavirus / neutralizing antibodies / fusion proteins / bunyavirus | ||||||
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 | Puumala orthohantavirus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Serris, A. / Rey, F.A. / Guardado-Calvo, P. | ||||||
Funding support | France, 1items
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Citation | Journal: Sci Transl Med / Year: 2023 Title: Structural and mechanistic basis of neutralization by a pan-hantavirus protective antibody. Authors: Mittler, E. / Serris, A. / Esterman, E.S. / Florez, C. / Polanco, L.C. / O'Brien, C.M. / Slough, M.M. / Tynell, J. / Groning, R. / Sun, Y. / Abelson, D.M. / Wec, A.Z. / Haslwanter, D. / ...Authors: Mittler, E. / Serris, A. / Esterman, E.S. / Florez, C. / Polanco, L.C. / O'Brien, C.M. / Slough, M.M. / Tynell, J. / Groning, R. / Sun, Y. / Abelson, D.M. / Wec, A.Z. / Haslwanter, D. / Keller, M. / Ye, C. / Bakken, R.R. / Jangra, R.K. / Dye, J.M. / Ahlm, C. / Rappazzo, C.G. / Ulrich, R.G. / Zeitlin, L. / Geoghegan, J.C. / Bradfute, S.B. / Sidoli, S. / Forsell, M.N.E. / Strandin, T. / Rey, F.A. / Herbert, A.S. / Walker, L.M. / Chandran, K. / Guardado-Calvo, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qqb.cif.gz | 436.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qqb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qqb_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7qqb_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7qqb_validation.xml.gz | 36 KB | Display | |
Data in CIF | 7qqb_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqb ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqb | HTTPS FTP |
-Related structure data
Related structure data | 6y5fS 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
-Protein / Antibody , 2 types, 4 molecules ABHL
#1: Protein | Mass: 95672.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Puumala orthohantavirus / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0B4U5I0, UniProt: A0A6M3W7M6 #2: Antibody | Mass: 31558.834 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) |
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-Sugars , 2 types, 3 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-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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#4: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 27 molecules
#5: Chemical | ChemComp-GOL / |
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#6: Water | ChemComp-HOH / |
-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 grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25%(w/v) PEG 1000, 0.1M Hepes 7.5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→39.89 Å / Num. obs: 43057 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.037 / Rrim(I) all: 0.126 / Net I/σ(I): 14.2 / Num. measured all: 495751 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y5F Resolution: 2.6→39 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 209.45 Å2 / Biso mean: 85.6355 Å2 / Biso min: 44.1 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→39 Å
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