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- PDB-6prl: Assembly of VIQKI P5(beta-L-homoproline) with human parainfluenza... -

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Basic information

Entry
Database: PDB / ID: 6prl
TitleAssembly of VIQKI P5(beta-L-homoproline) with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain
Components(Fusion glycoprotein F0) x 2
KeywordsANTIVIRAL PROTEIN / Fusion glycoprotein / six-helix bundle
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 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respirovirus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_torsion / struct_conn
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 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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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


Theoretical massNumber of molelcules
Total (without water)29,5966
Polymers29,5966
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Circular dichroism was used to detect a helical assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-116 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.521, 53.160, 58.231
Angle α, β, γ (deg.)90.000, 90.127, 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 F0


Mass: 5656.473 Da / Num. of mol.: 3 / Fragment: N-terminal heptad repeat domain / 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: 4208.922 Da / Num. of mol.: 3 / Fragment: C-terminal heptad repeat domain
Mutation: P453(beta-L-homoproline), E459V, A463I, D466Q, Q479K, K480I
Source method: obtained synthetically
Details: VIQKI P5(beta-L-homoproline) is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions P5(beta-L-homoproline), ...Details: VIQKI P5(beta-L-homoproline) is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions P5(beta-L-homoproline), E459V, A463I, D466Q, Q479K, and K480I. It is acetylated at the N-terminus and amidated at the C-terminus.
Source: (synth.) Human respirovirus 3 / References: UniProt: A0A0M3VGX6, UniProt: P06828*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.98 %
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; 100 mM imidazole/MES monohydrate (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: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.87→39.26 Å / Num. obs: 17950 / % possible obs: 98.82 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.96 Å2 / CC1/2: 0.971 / Rpim(I) all: 0.1134 / Rrim(I) all: 0.2977 / Rsym value: 0.2746 / Net I/σ(I): 8.57
Reflection shellResolution: 1.87→1.937 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.99 / Num. unique obs: 1687 / CC1/2: 0.568 / Rpim(I) all: 1.281 / Rrim(I) all: 3.064 / Rsym value: 2.765 / % possible all: 93.35

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Processing

Software
NameVersionClassification
PHASER1.13_2998phasing
xia2data reduction
DIALSdata scaling
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NRO

6nro


Resolution: 1.87→39.26 Å / SU ML: 0.2254 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.2786
RfactorNum. reflection% reflection
Rfree0.2509 1781 9.98 %
Rwork0.2026 --
obs0.2074 17845 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.36 Å2
Refinement stepCycle: LAST / Resolution: 1.87→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 0 164 2090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231935
X-RAY DIFFRACTIONf_angle_d0.43662602
X-RAY DIFFRACTIONf_chiral_restr0.0364325
X-RAY DIFFRACTIONf_plane_restr0.002321
X-RAY DIFFRACTIONf_dihedral_angle_d17.93541229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.35371260.27761118X-RAY DIFFRACTION91.4
1.92-1.980.25911370.25621236X-RAY DIFFRACTION98.14
1.98-2.040.32131340.25991212X-RAY DIFFRACTION98.9
2.04-2.110.3081330.23531239X-RAY DIFFRACTION99.06
2.11-2.20.25881410.22041241X-RAY DIFFRACTION99.35
2.2-2.30.25481340.20931213X-RAY DIFFRACTION99.04
2.3-2.420.31541400.20061255X-RAY DIFFRACTION99.5
2.42-2.570.2511370.19431239X-RAY DIFFRACTION99.71
2.57-2.770.22991410.20461261X-RAY DIFFRACTION99.93
2.77-3.050.23011320.19451255X-RAY DIFFRACTION100
3.05-3.490.23141400.18231242X-RAY DIFFRACTION100
3.49-4.390.19121410.15611273X-RAY DIFFRACTION99.93
4.39-39.260.25361450.20621280X-RAY DIFFRACTION99.3
Refinement TLS params.Method: refined / Origin x: 8.83291140456 Å / Origin y: -5.9204201643 Å / Origin z: 23.031264889 Å
111213212223313233
T0.0861292612375 Å2-0.0368489537019 Å20.0425446856064 Å2-0.0901357092588 Å2-0.0290674365426 Å2--0.112453808667 Å2
L1.70437098458 °20.165643855181 °2-0.557470506771 °2-0.569089328741 °2-0.0420288071695 °2--1.46552079806 °2
S0.0222489175507 Å °0.0592492179369 Å °-0.0909910064139 Å °0.0531597833222 Å °-0.04535563321 Å °0.00334475555748 Å °-0.0582210540859 Å °-0.0042223804275 Å °-0.0290394381946 Å °
Refinement TLS groupSelection details: all

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