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Yorodumi- PDB-6o40: Human parainfluenza virus type 3 fusion protein N-terminal heptad... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o40 | |||||||||
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Title | Human parainfluenza virus type 3 fusion protein N-terminal heptad repeat domain+VIQKI I454F I456F | |||||||||
Components | (Fusion glycoprotein F0) x 2 | |||||||||
Keywords | ANTIVIRAL PROTEIN / Fusion protein / fusion inhibitor / six-helix bundle | |||||||||
Function / homology | Function and homology information membrane => GO:0016020 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Human parainfluenza virus 3 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | |||||||||
Authors | Outlaw, V.K. / Gellman, S.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Structure-Guided Improvement of a Dual HPIV3/RSV Fusion Inhibitor. Authors: Outlaw, V.K. / Lemke, J.T. / Zhu, Y. / Gellman, S.H. / Porotto, M. / Moscona, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o40.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o40.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 6o40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o40_validation.pdf.gz | 416.6 KB | Display | wwPDB validaton report |
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Full document | 6o40_full_validation.pdf.gz | 416.5 KB | Display | |
Data in XML | 6o40_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 6o40_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/6o40 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/6o40 | HTTPS FTP |
-Related structure data
Related structure data | 6oj7C 6nroS 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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Unit cell |
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-Components
#1: Protein | Mass: 5656.473 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This compound is derived from residues 139-189 of the HPIV3 fusion glycoprotein. It is acetylated at the N-terminus and amidaxted at the C-terminus. Source: (synth.) Human parainfluenza virus 3 / References: UniProt: Q84193, UniProt: P06828*PLUS |
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#2: Protein/peptide | Mass: 4262.927 Da / Num. of mol.: 1 / Mutation: I454F, I456F, E459V, A463I, D466Q, Q479K, K480I / Source method: obtained synthetically Details: VIQKI I6F I8F is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions I454F, I456F, E459V, A463I, D466Q, ...Details: VIQKI I6F I8F is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions I454F, I456F, E459V, A463I, D466Q, Q479K, and K480I. It is acetylated at the N-terminus and amidaxted at the C-terminus. Source: (synth.) Human parainfluenza virus 3 / References: UniProt: A0A1L7B8S0, UniProt: P06828*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 30 mM NaF, 30 mM NaBr, 30 mM NaI, 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000 in 100 mM imidazole/MES monohydrate buffer (pH 6.5)20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000 in 100 mM ...Details: 30 mM NaF, 30 mM NaBr, 30 mM NaI, 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000 in 100 mM imidazole/MES monohydrate buffer (pH 6.5)20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000 in 100 mM imidazole/MES monohydrate buffer (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.197→28.37 Å / Num. obs: 21440 / % possible obs: 98.43 % / Redundancy: 9.8 % / Biso Wilson estimate: 16.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04153 / Rpim(I) all: 0.01325 / Rrim(I) all: 0.04364 / Net I/σ(I): 21.65 |
Reflection shell | Resolution: 1.197→1.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.7144 / Mean I/σ(I) obs: 1.55 / Num. unique obs: 1943 / CC1/2: 0.844 / Rpim(I) all: 0.4048 / Rrim(I) all: 0.8282 / % possible all: 88.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NRO Resolution: 1.2→28.37 Å / SU ML: 0.1435 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.2341
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→28.37 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -19.3930425183 Å / Origin y: 9.62952937786 Å / Origin z: -12.2978233908 Å
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Refinement TLS group | Selection details: all |