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- PDB-6ntx: Respiratory syncytial virus fusion protein N-terminal heptad repe... -

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Basic information

Entry
Database: PDB / ID: 6ntx
TitleRespiratory syncytial virus fusion protein N-terminal heptad repeat domain+VIQKI
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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: 2019
Title: Dual Inhibition of Human Parainfluenza Type 3 and Respiratory Syncytial Virus Infectivity with a Single Agent.
Authors: Outlaw, V.K. / Bottom-Tanzer, S. / Kreitler, D.F. / Gellman, S.H. / Porotto, M. / Moscona, A.
History
DepositionJan 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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


Theoretical massNumber of molelcules
Total (without water)19,5194
Polymers19,5194
Non-polymers00
Water36020
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)29,2786
Polymers29,2786
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11390 Å2
ΔGint-103 kcal/mol
Surface area10970 Å2
MethodPISA
2
B: Fusion glycoprotein F0
D: Fusion glycoprotein F0

B: Fusion glycoprotein F0
D: Fusion glycoprotein F0

B: Fusion glycoprotein F0
D: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)29,2786
Polymers29,2786
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area9130 Å2
ΔGint-89 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.967, 51.967, 299.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Components on special symmetry positions
IDModelComponents
11C-505-

HOH

21D-504-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 159 - 196 / Label seq-ID: 2 - 39

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 159 or (resid 160 and (name...AA
22(chain 'B' and (resid 159 through 185 or (resid 186...BB

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Components

#1: Protein Fusion glycoprotein F0


Mass: 5564.542 Da / Num. of mol.: 2 / Fragment: UNP residues 157-207 / Source method: obtained synthetically
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: 4194.895 Da / Num. of mol.: 2 / Fragment: UNP residues 449-484 / Mutation: E459V, A463I, D466Q, Q479K, K480I / Source method: obtained synthetically
Details: VIQKI is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions E459V, A463I, D466Q, Q479K and K480I. It is ...Details: VIQKI is a synthetic peptide derived from residues 449-484 of the HPIV3 fusion glycoprotein C-terminal heptad repeat domain with substitutions 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: A0A1V0BZ41, UniProt: P06828*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.99 Å3/Da / Density % sol: 38.22 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→44.1 Å / Num. obs: 8394 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 39.9 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.03028 / Rrim(I) all: 0.1297 / Rsym value: 0.1259 / Net I/σ(I): 15.34
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 16.9 % / Mean I/σ(I) obs: 2.43 / Num. unique obs: 829 / CC1/2: 0.863 / Rpim(I) all: 0.3936 / Rrim(I) all: 1.645 / Rsym value: 1.596 / % possible all: 99.64

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SADABSdata scaling
PROTEUM2data reduction
SAINTdata reduction
PHASERphasing
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KPE

3kpe


Resolution: 2.2→28.76 Å / SU ML: 0.2663 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.5828
RfactorNum. reflection% reflection
Rfree0.2846 837 10 %
Rwork0.2315 --
obs0.2367 8371 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 0 20 1047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01461029
X-RAY DIFFRACTIONf_angle_d1.28041392
X-RAY DIFFRACTIONf_chiral_restr0.0598182
X-RAY DIFFRACTIONf_plane_restr0.0113174
X-RAY DIFFRACTIONf_dihedral_angle_d22.105364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.29661360.27231223X-RAY DIFFRACTION99.93
2.34-2.520.26161360.22371221X-RAY DIFFRACTION100
2.52-2.770.29711390.21751246X-RAY DIFFRACTION99.93
2.77-3.170.28671370.22681236X-RAY DIFFRACTION99.93
3.17-40.21471420.20971277X-RAY DIFFRACTION99.86
4-28.760.33221470.2461331X-RAY DIFFRACTION99.13

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