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- PDB-6vjo: Human parainfluenza virus type 3 fusion glycoprotein N-terminal h... -

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Basic information

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


fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respirovirus 3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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: 2021
Title: Engineering Protease-Resistant Peptides to Inhibit Human Parainfluenza Viral Respiratory Infection.
Authors: Outlaw, V.K. / Cheloha, R.W. / Jurgens, E.M. / Bovier, F.T. / Zhu, Y. / Kreitler, D.F. / Harder, O. / Niewiesk, S. / Porotto, M. / Gellman, S.H. / Moscona, A.
History
DepositionJan 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 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 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)9,8482
Polymers9,8482
Non-polymers00
Water63135
1
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0

A: Fusion glycoprotein F0
B: Fusion glycoprotein F0

A: Fusion glycoprotein F0
B: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)29,5456
Polymers29,5456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area14900 Å2
ΔGint-133 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.345, 48.345, 134.546
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallA3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein/peptide Fusion glycoprotein F0


Mass: 4191.891 Da / Num. of mol.: 1
Mutation: I458(XCP), E459V, K462(XPC), A463I, S465(XCP), E469(B3E), E472(B3E), R476(XPC), Q479(XCP), S483(XCP)
Source method: obtained synthetically
Details: alpha/beta-VI is a synthetic alpha/beta peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions I458(XCP), E459V, K462(XPC), ...Details: alpha/beta-VI is a synthetic alpha/beta peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions I458(XCP), E459V, K462(XPC), A463I, S465(XCP), E469(B3E), E472(B3E), R476(XPC), Q479(XCP), S483(XCP). It is acetylated at the N-terminus and amidated at the C-terminus.
Source: (synth.) Human respirovirus 3 / References: UniProt: A0A1X9QNY3
#2: Protein Fusion glycoprotein F0


Mass: 5656.473 Da / Num. of mol.: 1 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→35.55 Å / Num. obs: 7675 / % possible obs: 96.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 16.48 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.058 / Rrim(I) all: 0.171 / Rsym value: 0.161 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.13 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1107 / CC1/2: 0.426 / Rpim(I) all: 0.478 / Rrim(I) all: 0.944 / Rsym value: 0.161 / % possible all: 83.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZTM

1ztm


Resolution: 2→35.55 Å / SU ML: 0.3378 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.9055
RfactorNum. reflection% reflection
Rfree0.2256 776 10.13 %
Rwork0.1996 --
obs0.2021 7660 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.3 Å2
Refinement stepCycle: LAST / Resolution: 2→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms665 0 0 35 700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052674
X-RAY DIFFRACTIONf_angle_d0.7454917
X-RAY DIFFRACTIONf_chiral_restr0.0361117
X-RAY DIFFRACTIONf_plane_restr0.0029116
X-RAY DIFFRACTIONf_dihedral_angle_d17.635241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.41661130.3966990X-RAY DIFFRACTION83.56
2.13-2.290.29171340.26421192X-RAY DIFFRACTION99.92
2.29-2.520.22871320.17751176X-RAY DIFFRACTION100
2.52-2.880.18961350.17041184X-RAY DIFFRACTION100
2.89-3.630.18951280.1711174X-RAY DIFFRACTION98.41
3.63-35.550.18481340.15951168X-RAY DIFFRACTION98.19
Refinement TLS params.Method: refined / Origin x: 40.9956304456 Å / Origin y: 27.6205915257 Å / Origin z: -12.3618099208 Å
111213212223313233
T0.0714114061446 Å2-0.00872840867024 Å2-0.00604962259941 Å2-0.120827383566 Å2-0.00582582508272 Å2--0.108728149411 Å2
L0.531188372509 °2-0.0640536512793 °2-0.104432518034 °2-0.50277149129 °20.390002075532 °2--2.12496776748 °2
S0.00407986816956 Å °0.0308678333427 Å °0.0200295953317 Å °-0.0803972125233 Å °0.0412449527367 Å °0.0715765334756 Å °0.0640240676534 Å °-0.544098619999 Å °0.00556540623083 Å °
Refinement TLS groupSelection details: all

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