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

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Basic information

Entry
Database: PDB / ID: 6nyx
TitleHuman parainfluenza virus type 3 fusion protein N-terminal heptad repeat domain+VI
Components(Fusion glycoprotein F0) x 2
KeywordsANTIVIRAL PROTEIN / Fusion protein / fusion inhibitor / six-helix bundle
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesHuman respirovirus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionFeb 12, 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: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
D: Fusion glycoprotein F0
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
G: Fusion glycoprotein F0
H: Fusion glycoprotein F0
I: Fusion glycoprotein F0
J: Fusion glycoprotein F0
K: Fusion glycoprotein F0
L: Fusion glycoprotein F0
M: Fusion glycoprotein F0
N: Fusion glycoprotein F0
O: Fusion glycoprotein F0
P: Fusion glycoprotein F0
Q: Fusion glycoprotein F0
T: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,98020
Polymers88,68018
Non-polymers3002
Water5,296294
1
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
M: Fusion glycoprotein F0
N: Fusion glycoprotein F0
O: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)29,5606
Polymers29,5606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-118 kcal/mol
Surface area10400 Å2
MethodPISA
2
D: Fusion glycoprotein F0
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
P: Fusion glycoprotein F0
Q: Fusion glycoprotein F0
T: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)29,5606
Polymers29,5606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-127 kcal/mol
Surface area10680 Å2
MethodPISA
3
G: Fusion glycoprotein F0
H: Fusion glycoprotein F0
hetero molecules

G: Fusion glycoprotein F0
H: Fusion glycoprotein F0
hetero molecules

G: Fusion glycoprotein F0
H: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1439
Polymers29,5606
Non-polymers5833
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area13480 Å2
ΔGint-129 kcal/mol
Surface area11590 Å2
MethodPISA
4
I: Fusion glycoprotein F0
J: Fusion glycoprotein F0

I: Fusion glycoprotein F0
J: Fusion glycoprotein F0

I: Fusion glycoprotein F0
J: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)29,5606
Polymers29,5606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13570 Å2
ΔGint-128 kcal/mol
Surface area10850 Å2
MethodPISA
5
K: Fusion glycoprotein F0
L: Fusion glycoprotein F0
hetero molecules

K: Fusion glycoprotein F0
L: Fusion glycoprotein F0
hetero molecules

K: Fusion glycoprotein F0
L: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8789
Polymers29,5606
Non-polymers3183
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area14070 Å2
ΔGint-106 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.030, 88.030, 75.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z

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Components

#1: Protein
Fusion glycoprotein F0


Mass: 5656.473 Da / Num. of mol.: 9 / 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 respirovirus 3 / References: UniProt: Q84193, UniProt: P06828*PLUS
#2: Protein/peptide
Fusion glycoprotein F0


Mass: 4196.825 Da / Num. of mol.: 9 / Fragment: UNP residues 449-484 / Mutation: E459V, A463I / Source method: obtained synthetically
Details: VI is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions E459V and A463I. It is acetylated at the N- ...Details: VI is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions E459V and A463I. It is acetylated at the N-terminus and amidated at the C-terminus.
Source: (synth.) Human respirovirus 3 / References: UniProt: Q84193, UniProt: P06828*PLUS
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2 Å3/Da / Density % sol: 38.48 %
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)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→38.12 Å / Num. obs: 56066 / % possible obs: 99.82 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.14 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03216 / Rrim(I) all: 0.07694 / Rsym value: 0.06986 / Net I/σ(I): 12.85
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 5640 / CC1/2: 0.66 / Rpim(I) all: 0.5373 / Rrim(I) all: 1.254 / Rsym value: 1.132 / % possible all: 99.96

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Processing

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

1ztm


Resolution: 1.85→38.12 Å / SU ML: 0.2386 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.7929
RfactorNum. reflection% reflection
Rfree0.2288 1693 3.02 %
Rwork0.1979 --
obs0.1988 55986 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.67 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 20 294 6089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01765829
X-RAY DIFFRACTIONf_angle_d1.56277842
X-RAY DIFFRACTIONf_chiral_restr0.0798970
X-RAY DIFFRACTIONf_plane_restr0.0151990
X-RAY DIFFRACTIONf_dihedral_angle_d19.60352266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.31991390.29744568X-RAY DIFFRACTION99.98
1.9-1.970.27951420.26334520X-RAY DIFFRACTION99.96
1.97-2.040.27461460.2594523X-RAY DIFFRACTION100
2.04-2.120.241420.23434519X-RAY DIFFRACTION99.96
2.12-2.210.21571420.20534501X-RAY DIFFRACTION99.91
2.21-2.330.21611300.19324567X-RAY DIFFRACTION100
2.33-2.480.2041370.1964530X-RAY DIFFRACTION99.96
2.48-2.670.22611450.18964522X-RAY DIFFRACTION99.91
2.67-2.940.23851380.20264532X-RAY DIFFRACTION100
2.94-3.360.21091460.19214506X-RAY DIFFRACTION99.94
3.36-4.230.18421480.16484534X-RAY DIFFRACTION99.91
4.23-38.130.28711380.20214471X-RAY DIFFRACTION98.44

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