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- PDB-6nro: Human parainfluenza virus type 3 fusion protein N-terminal heptad... -

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Basic information

Entry
Database: PDB / ID: 6nro
TitleHuman parainfluenza virus type 3 fusion protein N-terminal heptad repeat domain+VIQKI
Components
  • Human parainfluenza virus type 3 fusion glycoprotein C-terminal heptad repeat domain
  • Human parainfluenza virus type 3 fusion glycoprotein N-terminal heptad repeat domain
KeywordsANTIVIRAL 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
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fusion glycoprotein F0 / Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman parainfluenza virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOutlaw, V.K. / Kreitler, D.F. / Gellman, S.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM122263 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI114736 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
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
DepositionJan 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human parainfluenza virus type 3 fusion glycoprotein N-terminal heptad repeat domain
E: Human parainfluenza virus type 3 fusion glycoprotein N-terminal heptad repeat domain
C: Human parainfluenza virus type 3 fusion glycoprotein N-terminal heptad repeat domain
D: Human parainfluenza virus type 3 fusion glycoprotein C-terminal heptad repeat domain
B: Human parainfluenza virus type 3 fusion glycoprotein C-terminal heptad repeat domain
F: Human parainfluenza virus type 3 fusion glycoprotein C-terminal heptad repeat domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7008
Polymers29,5546
Non-polymers1462
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Circular dichroism spectroscopy was used to determine the formation of helical assemblies in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13630 Å2
ΔGint-136 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.970, 52.250, 54.110
Angle α, β, γ (deg.)90.000, 100.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Human parainfluenza virus type 3 fusion glycoprotein N-terminal heptad repeat domain


Mass: 5656.473 Da / Num. of mol.: 3 / Fragment: UNP residues 139-189 / 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 parainfluenza virus 3 / References: UniProt: A0A1V0E102, UniProt: P06828*PLUS
#2: Protein/peptide Human parainfluenza virus type 3 fusion glycoprotein C-terminal heptad repeat domain


Mass: 4194.895 Da / Num. of mol.: 3 / Fragment: 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.) Human parainfluenza virus 3 / References: UniProt: A0A023PHT3, UniProt: P06828*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.56 %
Crystal growTemperature: 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 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)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.75→39.293 Å / Num. obs: 22158 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 36.72 Å2 / CC1/2: 1 / Rpim(I) all: 0.01925 / Rrim(I) all: 0.04893 / Rsym value: 0.04488 / Net I/σ(I): 18.26
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 2189 / CC1/2: 0.726 / Rpim(I) all: 0.48 / Rrim(I) all: 1.238 / Rsym value: 1.139 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZTM

1ztm


Resolution: 1.75→39.293 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.83
RfactorNum. reflection% reflection
Rfree0.2444 1997 9.03 %
Rwork0.2167 --
obs0.2192 22122 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 305.93 Å2 / Biso mean: 54.3386 Å2 / Biso min: 26.48 Å2
Refinement stepCycle: final / Resolution: 1.75→39.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 18 83 2024
Biso mean--83.12 59.39 -
Num. residues----251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7501-1.79390.37771420.355714341576100
1.7939-1.84240.33471390.327414061545100
1.8424-1.89660.33331450.290214451590100
1.8966-1.95780.30021400.276814191559100
1.9578-2.02780.29221440.263814471591100
2.0278-2.1090.25941440.258214431587100
2.109-2.2050.26881420.238814301572100
2.205-2.32120.28121410.237514291570100
2.3212-2.46660.29151440.222914511595100
2.4666-2.6570.2091440.20914481592100
2.657-2.92430.26641400.2171419155999
2.9243-3.34730.22151450.213914611606100
3.3473-4.21640.20481430.178514441587100
4.2164-39.30270.24681440.21451449159396
Refinement TLS params.Method: refined / Origin x: -6.7167 Å / Origin y: -8.1854 Å / Origin z: -20.1981 Å
111213212223313233
T0.252 Å20.0114 Å2-0.0497 Å2-0.1926 Å20.0083 Å2--0.2742 Å2
L5.5601 °20.8838 °2-3.3551 °2-1.2164 °2-0.2135 °2--4.4733 °2
S-0.007 Å °-0.1215 Å °0.155 Å °-0.0184 Å °-0.0666 Å °0.0854 Å °-0.0237 Å °0.1098 Å °0.0586 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA141 - 190
2X-RAY DIFFRACTION1allA201
3X-RAY DIFFRACTION1allE141 - 189
4X-RAY DIFFRACTION1allC141 - 189
5X-RAY DIFFRACTION1allD451 - 484
6X-RAY DIFFRACTION1allB450 - 484
7X-RAY DIFFRACTION1allF451 - 501
8X-RAY DIFFRACTION1allS1 - 99

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