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

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Basic information

Entry
Database: PDB / ID: 6eaj
TitleCRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT T400A 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


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.851 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)64,60214
Polymers63,1881
Non-polymers1,41413
Water21612
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)193,80742
Polymers189,5653
Non-polymers4,24239
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area21540 Å2
ΔGint-373 kcal/mol
Surface area47680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.190, 168.190, 168.190
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-606-

SO4

21F-606-

SO4

31F-611-

SO4

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Components

#1: Protein Fusion glycoprotein F0


Mass: 63188.320 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain / Mutation: S155C, S290C, S190F, V207L, T400A
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.: 11 / 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.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.79 % / Mosaicity: 0.16 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 1.50M 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: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 2.85→56.06 Å / Num. obs: 19529 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 60.99 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.072 / Rrim(I) all: 0.159 / Net I/σ(I): 8.6 / Num. measured all: 92996 / Scaling rejects: 18
Reflection shellResolution: 2.85→3 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.974 / Num. unique obs: 2775 / CC1/2: 0.539 / Rpim(I) all: 0.489 / Rrim(I) all: 1.094 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EA4

5ea4


Resolution: 2.851→56.06 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.237 948 4.87 %
Rwork0.2045 --
obs0.2061 19472 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.91 Å2 / Biso mean: 60.1719 Å2 / Biso min: 24.49 Å2
Refinement stepCycle: final / Resolution: 2.851→56.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 78 12 3509
Biso mean--95.78 40.22 -
Num. residues----443
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8507-3.0010.35751490.31982534268399
3.001-3.1890.31231240.2622584270899
3.189-3.43520.27151300.24162594272499
3.4352-3.78080.27761310.195326212752100
3.7808-4.32770.22991230.175326622785100
4.3277-5.45170.18141480.165826772825100
5.4517-56.07420.21311430.205628522995100

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