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- PDB-6ead: CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLY... -

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Basic information

Entry
Database: PDB / ID: 6ead
TitleCRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT F140I STABILIZED IN THE PREFUSION STATE
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / CLASS I VIRAL FUSION PROTEIN / FUSION / RESPIRATORY SYNCYTIAL VIRUS / PREFUSION / FUSION INHIBITOR
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 / 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
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBattles, M.B. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32AI007519-18 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
CitationJournal: To be published
Title: Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance
Authors: Battles, M.B. / McLellan, J.S.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5666
Polymers63,7241
Non-polymers8425
Water19811
1
F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,69718
Polymers191,1723
Non-polymers2,52515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16060 Å2
ΔGint-92 kcal/mol
Surface area53760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.950, 168.950, 168.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11F-707-

HOH

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Components

#1: Protein Fusion glycoprotein F0


Mass: 63723.844 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain / Mutation: N67I, S215P, F140I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Plasmid: P(ALPHA)H / Production host: Homo sapiens (human) / Strain (production host): HEK293 FREESTYLE / References: UniProt: W8RJF9, UniProt: P03420*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.15 Å3/Da / Density % sol: 60.99 % / Mosaicity: 0.34 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 1.34M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 18, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→39.82 Å / Num. obs: 20909 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 83.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.034 / Rrim(I) all: 0.119 / Net I/σ(I): 15 / Num. measured all: 257637 / Scaling rejects: 55
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 12 % / Rmerge(I) obs: 1.987 / Num. unique obs: 2973 / CC1/2: 0.529 / Rpim(I) all: 0.598 / Rrim(I) all: 2.078 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C69

5c69


Resolution: 2.8→39.82 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.29
RfactorNum. reflection% reflection
Rfree0.2299 1026 4.92 %
Rwork0.2013 --
obs0.2028 20866 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 235.48 Å2 / Biso mean: 91.6912 Å2 / Biso min: 41.11 Å2
Refinement stepCycle: final / Resolution: 2.8→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 51 11 3535
Biso mean--166.22 61.94 -
Num. residues----450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8003-2.94790.38981540.327727512905
2.9479-3.13250.32871450.286927732918
3.1325-3.37430.28641420.264527792921
3.3743-3.71360.29411470.22227932940
3.7136-4.25050.28231330.198228412974
4.2505-5.35310.17231470.162328603007
5.3531-39.82590.18711580.182630433201

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