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Yorodumi- PDB-7lyd: Crystal Structure of Ebola zaire Envelope glycoprotein GP in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lyd | ||||||
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Title | Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SSGCID / Envelope glycoprotein / Zaire ebolavirus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Zaire ebolavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: to be published Title: Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146 Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lyd.cif.gz | 172 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lyd.ent.gz | 132.5 KB | Display | PDB format |
PDBx/mmJSON format | 7lyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/7lyd ftp://data.pdbj.org/pub/pdb/validation_reports/ly/7lyd | HTTPS FTP |
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-Related structure data
Related structure data | 6f5uS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32309.303 Da / Num. of mol.: 1 / Fragment: EbzaA.19907.a.HE11 proteolyzed N-terminal domain / Mutation: T42A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: GP / Plasmid: EbzaA.19907.a.HE11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05320 |
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#2: Protein | Mass: 18922.320 Da / Num. of mol.: 1 / Fragment: EbzaA.19907.a.HE11 proteolyzed C-terminal domain / Mutation: H613A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: GP / Plasmid: EbzaA.19907.a.HE11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05320 |
-Sugars , 2 types, 5 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-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: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 183 molecules
#5: Chemical | ChemComp-YOD / ( | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Sequence details | Residues in the C-terminal portion of chain A were difficult to identify, and so were modeled as ...Residues in the C-terminal portion of chain A were difficult to identify, and so were modeled as UNK. The actual sequence for chain A is: ETGRSIPLGV |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.6 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Molecular Dimensions/Calibre Morpheus screen A11: 10% (w/V) PEG 4000, 20% (V/V) glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM bicine/Trizma base pH 8.5: EbzaA.19907.a. ...Details: Molecular Dimensions/Calibre Morpheus screen A11: 10% (w/V) PEG 4000, 20% (V/V) glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM bicine/Trizma base pH 8.5: EbzaA.19907.a.HE11.PD38351 at 10.61 mg/ml: over night soak with 1mM compound ARN0075146 (BSI110990): tray 313149a11, cryo: direct: puck hdp6-5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 14, 2019 / Details: Beryllium Lenses |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 32679 / % possible obs: 99.9 % / Redundancy: 6.824 % / Biso Wilson estimate: 54.11 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.26 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 6.91 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 2366 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6F5U Resolution: 2.35→41.63 Å / SU ML: 0.267 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.961 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: 65.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→41.63 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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