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- PDB-6pyq: Assembly of VIQKI D455(beta-L-homoaspartic acid)with human parain... -

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Basic information

Entry
Database: PDB / ID: 6pyq
TitleAssembly of VIQKI D455(beta-L-homoaspartic acid)with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain
Components
  • Fusion glycoprotein F1
  • synthetic peptide derived from Fusion glycoprotein F1
KeywordsVIRAL PROTEIN / Fusion glycoprotein / six-helix bundle / foldamer
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
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respirovirus 3
Human parainfluenza 3 virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 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 / 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
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

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F1
B: synthetic peptide derived from Fusion glycoprotein F1
C: Fusion glycoprotein F1
D: synthetic peptide derived from Fusion glycoprotein F1
E: Fusion glycoprotein F1
F: synthetic peptide derived from Fusion glycoprotein F1


Theoretical massNumber of molelcules
Total (without water)29,5966
Polymers29,5966
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Circular dichroism spectroscopy was used to determine the presence of a helical assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint-95 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.850, 49.340, 56.180
Angle α, β, γ (deg.)90.000, 103.610, 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 respirovirus 3 / References: UniProt: Q84193, UniProt: P06828*PLUS
#2: Protein/peptide synthetic peptide derived from Fusion glycoprotein F1


Mass: 4208.921 Da / Num. of mol.: 3
Mutation: D455(beta-L-homoaspartic acid), 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 / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.81 Å3/Da / Density % sol: 32.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM imidazole/MES monohydrate (pH 6.5), 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: 0.9786 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: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.79→24.73 Å / Num. obs: 20102 / % possible obs: 99.76 % / Redundancy: 8.5 % / Biso Wilson estimate: 29.85 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.031 / Rrim(I) all: 0.089 / Rsym value: 0.084 / Net I/σ(I): 13.7
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1037 / CC1/2: 0.395 / Rpim(I) all: 0.732 / Rrim(I) all: 2.151 / Rsym value: 2.021 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NRO

6nro


Resolution: 1.79→24.73 Å / SU ML: 0.1929 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6996
RfactorNum. reflection% reflection
Rfree0.2321 1998 9.95 %
Rwork0.2067 --
obs0.2091 20082 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.58 Å2
Refinement stepCycle: LAST / Resolution: 1.79→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 0 54 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01451853
X-RAY DIFFRACTIONf_angle_d1.4052495
X-RAY DIFFRACTIONf_chiral_restr0.0862303
X-RAY DIFFRACTIONf_plane_restr0.0149316
X-RAY DIFFRACTIONf_dihedral_angle_d18.39111187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.33111440.33431293X-RAY DIFFRACTION99.79
1.83-1.880.31481410.28091285X-RAY DIFFRACTION99.93
1.88-1.940.29181410.24971273X-RAY DIFFRACTION99.79
1.94-20.23561440.24271303X-RAY DIFFRACTION99.72
2-2.070.25191410.22561286X-RAY DIFFRACTION99.86
2.07-2.160.21471420.20241280X-RAY DIFFRACTION99.72
2.16-2.250.21681440.18621295X-RAY DIFFRACTION99.93
2.25-2.370.18531400.17741274X-RAY DIFFRACTION100
2.37-2.520.18881440.17451304X-RAY DIFFRACTION100
2.52-2.720.26421420.18121280X-RAY DIFFRACTION99.79
2.72-2.990.20671440.19881305X-RAY DIFFRACTION99.93
2.99-3.420.23641420.19861291X-RAY DIFFRACTION99.93
3.42-4.310.19671460.17521319X-RAY DIFFRACTION99.86
4.31-24.730.2721430.25111296X-RAY DIFFRACTION97.03
Refinement TLS params.Method: refined / Origin x: 13.0066805196 Å / Origin y: 4.74655574207 Å / Origin z: 18.1354917334 Å
111213212223313233
T0.15900920509 Å20.0186441962877 Å2-0.0473562095482 Å2-0.114857929214 Å20.0193254682462 Å2--0.209414827261 Å2
L3.72301259445 °20.49583642181 °2-1.45923271752 °2-1.88750563307 °20.33375398834 °2--3.30330359357 °2
S0.0584311507602 Å °0.225902043642 Å °0.00772872121257 Å °-0.0279021266974 Å °0.0182336108486 Å °-0.0835279510726 Å °-0.0282573637702 Å °-0.0177102037322 Å °-0.0695076862009 Å °
Refinement TLS groupSelection details: all

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