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- PDB-6pz6: Co-assembly of VIQKI D452(beta-L-homoaspartic acid) with human pa... -

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Basic information

Entry
Database: PDB / ID: 6pz6
TitleCo-assembly of VIQKI D452(beta-L-homoaspartic acid) with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain
Components
  • Fusion glycoprotein F1
  • VIQKI D4(beta-L-homoaspartic acid) synthetic peptid derived from Fusion glycoprotein F1e
KeywordsVIRAL PROTEIN / Fusion glycoprotein / six-helix bundle
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: 1.7 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 31, 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
Revision 2.1Jul 10, 2024Group: Data collection / Category: chem_comp / Item: _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F1
B: VIQKI D4(beta-L-homoaspartic acid) synthetic peptid derived from Fusion glycoprotein F1e
C: Fusion glycoprotein F1
D: VIQKI D4(beta-L-homoaspartic acid) synthetic peptid derived from Fusion glycoprotein F1e
E: Fusion glycoprotein F1
F: VIQKI D4(beta-L-homoaspartic acid) synthetic peptid derived from Fusion glycoprotein F1e


Theoretical massNumber of molelcules
Total (without water)29,5966
Polymers29,5966
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Circular dichroism spectroscopy was used to determine the presence of helical assemblies in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-119 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.640, 52.450, 55.620
Angle α, β, γ (deg.)90.000, 99.200, 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 VIQKI D4(beta-L-homoaspartic acid) synthetic peptid derived from Fusion glycoprotein F1e


Mass: 4208.921 Da / Num. of mol.: 3
Mutation: D452(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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.09 Å3/Da / Density % sol: 36.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30 mM NaF, 30 mM NaBr, 30 mM NaI, 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: 0.9786 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: 1.7→27.45 Å / Num. obs: 24510 / % possible obs: 98.44 % / Redundancy: 7.5 % / Biso Wilson estimate: 36.94 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Rsym value: 0.045 / Net I/σ(I): 19.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1206 / CC1/2: 0.552 / Rpim(I) all: 0.698 / Rrim(I) all: 1.94 / Rsym value: 1.809 / % possible all: 98.29

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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: 1.7→27.45 Å / SU ML: 0.2363 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6355 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2545 1999 8.16 %
Rwork0.2276 22501 -
obs0.2298 24500 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 0 53 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481901
X-RAY DIFFRACTIONf_angle_d0.63072556
X-RAY DIFFRACTIONf_chiral_restr0.0417315
X-RAY DIFFRACTIONf_plane_restr0.0031316
X-RAY DIFFRACTIONf_dihedral_angle_d14.32151212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.36711400.36381580X-RAY DIFFRACTION97.56
1.74-1.790.36431410.35121583X-RAY DIFFRACTION98.01
1.79-1.840.35221390.31371565X-RAY DIFFRACTION97.54
1.84-1.90.31331430.29771609X-RAY DIFFRACTION97.39
1.9-1.970.2951380.29491549X-RAY DIFFRACTION95.96
1.97-2.050.30541420.26571605X-RAY DIFFRACTION98.42
2.05-2.140.25851410.24711587X-RAY DIFFRACTION98.35
2.14-2.250.25271430.23271613X-RAY DIFFRACTION98.54
2.25-2.40.23561430.2391603X-RAY DIFFRACTION99.2
2.4-2.580.23181450.22621631X-RAY DIFFRACTION99.72
2.58-2.840.26851450.23531649X-RAY DIFFRACTION99.67
2.84-3.250.26121470.22361633X-RAY DIFFRACTION99.83
3.25-4.090.24611460.20231653X-RAY DIFFRACTION99.89
4.09-27.450.23691460.2141641X-RAY DIFFRACTION97.49
Refinement TLS params.Method: refined / Origin x: 8.02676158148 Å / Origin y: -8.6869258004 Å / Origin z: 6.9641010044 Å
111213212223313233
T0.304715215464 Å20.0187870003007 Å2-0.0674945579455 Å2-0.18562804312 Å20.0145402925023 Å2--0.29397900228 Å2
L5.46166853508 °20.080538624306 °2-2.88156317706 °2-0.944654245925 °20.430794361962 °2--4.22630592627 °2
S0.00976987827421 Å °-0.102831197103 Å °-0.0339989146538 Å °-0.0733396712584 Å °-0.127203593413 Å °0.0995031469035 Å °-0.0687665434686 Å °-0.085852397126 Å °0.102564028859 Å °
Refinement TLS groupSelection details: all

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