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- PDB-6ntx: Respiratory syncytial virus fusion protein N-terminal heptad repe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ntx | |||||||||
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Title | Respiratory syncytial virus fusion protein N-terminal heptad repeat domain+VIQKI | |||||||||
![]() | (Fusion glycoprotein F0) x 2 | |||||||||
![]() | ANTIVIRAL PROTEIN / Fusion protein / fusion inhibitor / six-helix bundle | |||||||||
Function / homology | ![]() positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Outlaw, V.K. / Kreitler, D.F. / Gellman, S.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Dual Inhibition of Human Parainfluenza Type 3 and Respiratory Syncytial Virus Infectivity with a Single Agent. Authors: Outlaw, V.K. / Bottom-Tanzer, S. / Kreitler, D.F. / Gellman, S.H. / Porotto, M. / Moscona, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.2 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nroC ![]() 6nyxC ![]() 3kpeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 159 - 196 / Label seq-ID: 2 - 39
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Components
#1: Protein | Mass: 5564.542 Da / Num. of mol.: 2 / Fragment: UNP residues 157-207 / Source method: obtained synthetically Details: This compound is derived from the the RSV-A2 fusion glycoprotein N-terminal heptad repeat domain residues 158-208. It is acetylated at the N-terminus and amidated at the C-terminus. Source: (synth.) ![]() #2: Protein/peptide | Mass: 4194.895 Da / Num. of mol.: 2 / Fragment: UNP residues 449-484 / Mutation: E459V, A463I, D466Q, Q479K, K480I / Source method: obtained synthetically Details: VIQKI is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions E459V, A463I, D466Q, Q479K and K480I. It is ...Details: VIQKI is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions E459V, A463I, D466Q, Q479K and K480I. It is acetylated at the N-terminus and amidated at the C-terminus. Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30 mM NaF, 30 mM NaBr, 30 mM NaI, 12.5% (v/v) 2-methyl-2,4-pentanediol, 12.5% (v/v) PEG 1000, 12.5% (w/v) PEG 3350 in 100 mM NaHEPES/MOPS buffer (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Aug 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→44.1 Å / Num. obs: 8394 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 39.9 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.03028 / Rrim(I) all: 0.1297 / Rsym value: 0.1259 / Net I/σ(I): 15.34 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 16.9 % / Mean I/σ(I) obs: 2.43 / Num. unique obs: 829 / CC1/2: 0.863 / Rpim(I) all: 0.3936 / Rrim(I) all: 1.645 / Rsym value: 1.596 / % possible all: 99.64 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KPE Resolution: 2.2→28.76 Å / SU ML: 0.2663 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.5828
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→28.76 Å
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Refine LS restraints |
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LS refinement shell |
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