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- PDB-6oj7: Respiratory syncytial virus fusion glycoprotein N-terminal heptad... -

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Basic information

Entry
Database: PDB / ID: 6oj7
TitleRespiratory syncytial virus fusion glycoprotein N-terminal heptad repeat domain+VIQKI I456F
Components(Fusion glycoprotein F0) x 2
KeywordsANTIVIRAL PROTEIN / Fusion protein / fusion inhibitor / six-helix bundle
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane ...positive regulation of syncytium formation by virus / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0 / Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Human respirovirus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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)1RO1AI114736 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Structure-Guided Improvement of a Dual HPIV3/RSV Fusion Inhibitor.
Authors: Outlaw, V.K. / Lemke, J.T. / Zhu, Y. / Gellman, S.H. / Porotto, M. / Moscona, A.
History
DepositionApr 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F0
C: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)9,7932
Polymers9,7932
Non-polymers00
Water1,17165
1
A: Fusion glycoprotein F0
C: Fusion glycoprotein F0

A: Fusion glycoprotein F0
C: Fusion glycoprotein F0

A: Fusion glycoprotein F0
C: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)29,3806
Polymers29,3806
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13580 Å2
ΔGint-124 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.285, 32.285, 203.841
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
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 Fusion glycoprotein F0


Mass: 5564.542 Da / Num. of mol.: 1 / Fragment: N-terminal / Source method: obtained synthetically
Details: Compound details: This compound is derived from the the RSV-A2 fusion glycoprotein N-terminal heptad repeat domain residues 158-208. It is acetylated at the N-terminus and amidated at the C-terminus.
Source: (synth.) Human respiratory syncytial virus A / References: UniProt: A0A1U8ZTH8, UniProt: P03420*PLUS
#2: Protein/peptide Fusion glycoprotein F0


Mass: 4228.911 Da / Num. of mol.: 1 / Fragment: UNP residues 449-484 / Mutation: I456F, E459V, A463I, D466Q, Q479K, K480I / Source method: obtained synthetically
Details: VIQKI I454F is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions I454F, I456F, E459V, A463I, D466Q, Q479K, ...Details: VIQKI I454F is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions I454F, I456F, 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: A0A1X9QNS5, UniProt: P06828*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30 mM NaF, 30 mM NaBr, 30 mM NaI, 12.5% (v/v) 2-methyl-2,4-pentanediol, 12.5% (v/v) PEG 1000, 12.5% (w/v) PEG 3350 in 100 mM NaHEPES/MOPS buffer (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127231 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127231 Å / Relative weight: 1
ReflectionResolution: 1.45→26.96 Å / Num. obs: 13875 / % possible obs: 98.55 % / Redundancy: 9.86 % / Biso Wilson estimate: 19.28 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.0374 / Rrim(I) all: 0.12 / Net I/σ(I): 9.19
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 1262 / CC1/2: 0.399 / Rpim(I) all: 0.366 / Rrim(I) all: 0.929 / % possible all: 89.01

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Processing

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

6ntx


Resolution: 1.45→26.96 Å / SU ML: 0.1803 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.4085
RfactorNum. reflection% reflection
Rfree0.1887 1374 9.91 %
Rwork0.1793 --
obs0.1802 13869 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.05 Å2
Refinement stepCycle: LAST / Resolution: 1.45→26.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms641 0 0 65 706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125652
X-RAY DIFFRACTIONf_angle_d1.6865880
X-RAY DIFFRACTIONf_chiral_restr0.0869111
X-RAY DIFFRACTIONf_plane_restr0.0115108
X-RAY DIFFRACTIONf_dihedral_angle_d14.7878249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.50.35311220.29941121X-RAY DIFFRACTION88.66
1.5-1.560.28081330.24151238X-RAY DIFFRACTION98.42
1.56-1.630.23671410.22761279X-RAY DIFFRACTION100
1.63-1.720.21451420.22371268X-RAY DIFFRACTION100
1.72-1.830.25811480.21911263X-RAY DIFFRACTION99.86
1.83-1.970.25181330.19651262X-RAY DIFFRACTION99.93
1.97-2.170.22241410.17171275X-RAY DIFFRACTION99.16
2.17-2.480.17081430.15661263X-RAY DIFFRACTION100
2.48-3.120.16961370.16451257X-RAY DIFFRACTION100
3.12-26.970.15491340.16721269X-RAY DIFFRACTION98.53
Refinement TLS params.Method: refined / Origin x: 1.17329727507 Å / Origin y: 6.92552153942 Å / Origin z: 10.4728440421 Å
111213212223313233
T0.0964079658471 Å2-0.0203412312548 Å20.0132694947419 Å2-0.0854256899868 Å20.0159852562744 Å2--0.164289879633 Å2
L1.40981234261 °20.0862175934899 °20.819445470606 °2-1.50707202331 °21.26816353352 °2--8.02728524476 °2
S-0.00974327508285 Å °0.13735836226 Å °0.0968303383682 Å °-0.184811748059 Å °-0.0358296490991 Å °-0.000749874886269 Å °-0.210919536709 Å °0.0123409982577 Å °0.0502862951464 Å °
Refinement TLS groupSelection details: all

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