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

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Basic information

Entry
Database: PDB / ID: 6eae
TitleCRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT L141W 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 / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / 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 / 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: 2.9 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 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7268
Polymers63,8311
Non-polymers8957
Water00
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)194,17724
Polymers191,4933
Non-polymers2,68521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area19850 Å2
ΔGint-240 kcal/mol
Surface area49380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.190, 167.190, 167.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Fusion glycoprotein F0


Mass: 63830.906 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain / Mutation: N67I, S215P, L141W
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM

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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: 3.05 Å3/Da / Density % sol: 59.68 % / Mosaicity: 0.22 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 1.44M 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: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50.41 Å / Num. obs: 18328 / % possible obs: 100 % / Redundancy: 17.6 % / Biso Wilson estimate: 78.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.039 / Rrim(I) all: 0.165 / Net I/σ(I): 14 / Num. measured all: 323166 / Scaling rejects: 12
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 18.7 % / Rmerge(I) obs: 1.743 / Num. unique obs: 2903 / CC1/2: 0.607 / Rpim(I) all: 0.412 / Rrim(I) all: 1.792 / % 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: 2.9→46.37 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.65
RfactorNum. reflection% reflection
Rfree0.2259 885 4.84 %
Rwork0.1987 --
obs0.2002 18285 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 217.15 Å2 / Biso mean: 88.8756 Å2 / Biso min: 34.97 Å2
Refinement stepCycle: final / Resolution: 2.9→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 51 0 3540
Biso mean--112.05 --
Num. residues----451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9003-3.0820.3191430.295328272970
3.082-3.31990.32121450.268128362981
3.3199-3.65390.22641540.21328382992
3.6539-4.18230.26241320.194128913023
4.1823-5.26810.17021510.1629193070
5.2681-46.37610.21441600.192230893249
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.60541.0981-0.1461.35650.33740.5175-0.66541.2097-0.2355-0.34950.50160.1559-0.34380.23350.13840.5749-0.09880.07840.6626-0.08610.560312.24083.1461-7.4891
24.01751.53562.88391.45051.71582.5455-0.4210.27340.6801-0.4513-0.07710.649-0.229-0.0720.47940.8651-0.1709-0.1520.74520.03270.7227-2.076911.2644-9.6105
31.41461.8348-1.82667.4047-0.4192.9831-0.31751.55060.5016-1.23470.41540.9976-1.10420.8126-0.08971.4903-0.4292-0.29651.7682-0.08010.5068-4.8425.1386-28.1391
46.20860.94732.87591.5570.64191.0328-0.30681.2711-0.4289-0.53340.2770.07220.23560.2104-0.06380.7647-0.24150.01350.7942-0.0930.50429.95642.5308-9.2811
52.04920.2267-0.43443.1874-2.12584.4179-0.0931-0.1005-0.4308-0.29380.0219-0.45050.43170.31540.03540.4251-0.0020.04570.429-0.00830.569229.32192.052914.0884
68.2522-0.08550.91564.46841.04859.0206-0.4809-0.96270.92960.49960.3222-1.0705-1.490.90610.1120.6043-0.1424-0.20920.7713-0.05450.760536.434119.711625.6807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 27 through 73 )F27 - 73
2X-RAY DIFFRACTION2chain 'F' and (resid 74 through 157 )F74 - 157
3X-RAY DIFFRACTION3chain 'F' and (resid 158 through 216 )F158 - 216
4X-RAY DIFFRACTION4chain 'F' and (resid 217 through 328 )F217 - 328
5X-RAY DIFFRACTION5chain 'F' and (resid 329 through 469 )F329 - 469
6X-RAY DIFFRACTION6chain 'F' and (resid 470 through 506 )F470 - 506

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