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Yorodumi- PDB-6prl: Assembly of VIQKI P5(beta-L-homoproline) with human parainfluenza... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6prl | |||||||||
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Title | Assembly of VIQKI P5(beta-L-homoproline) with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain | |||||||||
Components | (Fusion glycoprotein F0) x 2 | |||||||||
Keywords | ANTIVIRAL PROTEIN / Fusion glycoprotein / 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 respirovirus 3 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | |||||||||
Authors | Outlaw, V.K. / Gellman, S.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Infect Dis. / Year: 2020 Title: Effects of Single alpha-to-beta Residue Replacements on Recognition of an Extended Segment in a Viral Fusion Protein. Authors: Outlaw, V.K. / Kreitler, D.F. / Stelitano, D. / Porotto, M. / Moscona, A. / Gellman, S.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6prl.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6prl.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 6prl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/6prl ftp://data.pdbj.org/pub/pdb/validation_reports/pr/6prl | HTTPS FTP |
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-Related structure data
Related structure data | 6pyqC 6pz6C 6v3vC 6vasC 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.: 3 / Fragment: N-terminal heptad repeat domain / 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 amidated at the C-terminus. Source: (synth.) Human respirovirus 3 / References: UniProt: Q84193, UniProt: P06828*PLUS #2: Protein/peptide | Mass: 4208.922 Da / Num. of mol.: 3 / Fragment: C-terminal heptad repeat domain Mutation: P453(beta-L-homoproline), E459V, A463I, D466Q, Q479K, K480I Source method: obtained synthetically Details: VIQKI P5(beta-L-homoproline) is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions P5(beta-L-homoproline), ...Details: VIQKI P5(beta-L-homoproline) is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions P5(beta-L-homoproline), E459V, A463I, D466Q, Q479K, and K480I. It is acetylated at the N-terminus and amidated at the C-terminus. Source: (synth.) Human respirovirus 3 / References: UniProt: A0A0M3VGX6, UniProt: P06828*PLUS #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.95 Å3/Da / Density % sol: 36.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30 mM NaF; 30 mM NaBr; 30 mM NaI; 20% v/v PEG 500 MME; 10 % w/v PEG 20000; 100 mM imidazole/MES monohydrate (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 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→39.26 Å / Num. obs: 17950 / % possible obs: 98.82 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.96 Å2 / CC1/2: 0.971 / Rpim(I) all: 0.1134 / Rrim(I) all: 0.2977 / Rsym value: 0.2746 / Net I/σ(I): 8.57 |
Reflection shell | Resolution: 1.87→1.937 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.99 / Num. unique obs: 1687 / CC1/2: 0.568 / Rpim(I) all: 1.281 / Rrim(I) all: 3.064 / Rsym value: 2.765 / % possible all: 93.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NRO Resolution: 1.87→39.26 Å / SU ML: 0.2254 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.2786
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→39.26 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: 8.83291140456 Å / Origin y: -5.9204201643 Å / Origin z: 23.031264889 Å
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Refinement TLS group | Selection details: all |