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- PDB-6v3v: Assembly of VIQKI I456(beta-L-homoisoleucine)with human parainflu... -

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Basic information

Entry
Database: PDB / ID: 6v3v
TitleAssembly of VIQKI I456(beta-L-homoisoleucine)with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain
Components(Fusion glycoprotein F1) x 2
KeywordsVIRAL PROTEIN / Fusion glycoprotein / six-helix bundle / foldamer
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHuman parainfluenza 3 virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsOutlaw, V.K. / 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: 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
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F1
B: Fusion glycoprotein F1
C: Fusion glycoprotein F1
D: Fusion glycoprotein F1
E: Fusion glycoprotein F1
F: Fusion glycoprotein F1


Theoretical massNumber of molelcules
Total (without water)29,5966
Polymers29,5966
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Circular dichroism spectroscopy was used to identify the formation of this assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-120 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.340, 52.200, 56.660
Angle α, β, γ (deg.)90.000, 98.420, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fusion glycoprotein F1


Mass: 5656.473 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Human parainfluenza 3 virus (strain Wash/47885/57)
References: UniProt: P06828
#2: Protein/peptide Fusion glycoprotein F1


Mass: 4208.922 Da / Num. of mol.: 3
Mutation: I456(beta-L-homoisoleucine), E459V, A463I, D466Q, Q479K, K480I
Source method: obtained synthetically
Source: (synth.) Human parainfluenza 3 virus (strain Wash/47885/57)
References: UniProt: P06828
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM HEPES/MOPS buffer (pH 7.5), 12.5% PEG1000, 12.5% PEG3350, 12.5% 2-methyl-2,4-pentanediol

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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: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.17→28.02 Å / Num. obs: 12097 / % possible obs: 99.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 52.31 Å2 / CC1/2: 1 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Rsym value: 0.067 / Net I/σ(I): 15.31
Reflection shellResolution: 2.17→2.248 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.17 / Num. unique obs: 1195 / CC1/2: 0.521 / Rpim(I) all: 0.7275 / Rrim(I) all: 2.008 / Rsym value: 1.87 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NRO

6nro


Resolution: 2.17→28.02 Å / SU ML: 0.355 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.1648
RfactorNum. reflection% reflection
Rfree0.2875 1209 9.99 %
Rwork0.2406 --
obs0.2453 12097 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 76.63 Å2
Refinement stepCycle: LAST / Resolution: 2.17→28.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 0 10 1906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021905
X-RAY DIFFRACTIONf_angle_d0.39452568
X-RAY DIFFRACTIONf_chiral_restr0.0449322
X-RAY DIFFRACTIONf_plane_restr0.0028323
X-RAY DIFFRACTIONf_dihedral_angle_d16.5281720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.260.38771340.34951206X-RAY DIFFRACTION99.55
2.26-2.360.3311330.30171197X-RAY DIFFRACTION99.85
2.36-2.480.3231340.26761206X-RAY DIFFRACTION99.85
2.48-2.640.36711340.26171205X-RAY DIFFRACTION99.93
2.64-2.840.34861350.28261216X-RAY DIFFRACTION99.93
2.84-3.130.30541340.26191198X-RAY DIFFRACTION99.78
3.13-3.580.30371360.25221229X-RAY DIFFRACTION99.85
3.58-4.510.21671340.20131203X-RAY DIFFRACTION99.55
4.51-28.020.29281350.22981229X-RAY DIFFRACTION97.71
Refinement TLS params.Method: refined / Origin x: -7.73623289111 Å / Origin y: -6.0967237848 Å / Origin z: -6.92619532569 Å
111213212223313233
T0.368071503468 Å2-0.025864448399 Å2-0.0990838541886 Å2-0.303765453232 Å2-0.0107077533668 Å2--0.418098589603 Å2
L8.86443072928 °2-0.279332172346 °2-6.70749756555 °2-1.8482727899 °2-0.708322811816 °2--8.89782769175 °2
S0.110089078013 Å °-0.0267378127244 Å °0.196903887307 Å °-0.0458077974406 Å °-0.0879196464857 Å °-0.082515480059 Å °-0.046538479785 Å °0.393643386935 Å °-0.0520560465141 Å °
Refinement TLS groupSelection details: all

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