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- PDB-5ea8: Crystal Structure of Prefusion RSV F Glycoprotein Fusion Inhibito... -

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Basic information

Entry
Database: PDB / ID: 5ea8
TitleCrystal Structure of Prefusion RSV F Glycoprotein Fusion Inhibitor Resistance Mutant D489Y
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / Class I viral fusion protein / fusion / respiratory syncytial virus / prefusion / fusion inhibitor
Function / homology
Function and homology information


Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / 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 ...Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / 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
D(-)-TARTARIC ACID / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBattles, M.B. / McLellan, J.S. / Arnoult, E. / Roymans, D. / Langedijk, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Charles H. Hood Foundation United States
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Molecular mechanism of respiratory syncytial virus fusion inhibitors.
Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / ...Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / Arnoult, E. / Peeples, M.E. / Roymans, D. / McLellan, J.S.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)64,1048
Polymers63,2661
Non-polymers8387
Water1,17165
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)192,31224
Polymers189,7993
Non-polymers2,51321
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_645z+1,x-1,y1
crystal symmetry operation9_654y+1,z,x-11
Buried area17750 Å2
ΔGint-252 kcal/mol
Surface area51190 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-759-

HOH

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 63266.430 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain (UNP residues 1-513) / Mutation: S190F, V207L, S155C, S290C, D489Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Plasmid: p(alpha)H / Cell line (production host): HEK293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P03420
#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.: 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.: 65 / 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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.54 M potassium/sodium tartrate, 0.2 M lithium sulfate, 0.1 M CHES, pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→48.55 Å / Num. obs: 25647 / % possible obs: 100 % / Redundancy: 29.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.042 / Net I/σ(I): 18.2 / Num. measured all: 752182 / Scaling rejects: 1161
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.6-2.7328.42.871.69489833420.5560.545100
8.62-48.5527.20.03665.42260383110.00799.5

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MMS

4mms


Resolution: 2.6→48.55 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 1282 5.01 %Random selection
Rwork0.1994 24293 --
obs0.2013 25575 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.04 Å2 / Biso mean: 67.3822 Å2 / Biso min: 23.99 Å2
Refinement stepCycle: final / Resolution: 2.6→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 48 65 3584
Biso mean--113.26 49.77 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063572
X-RAY DIFFRACTIONf_angle_d0.9324831
X-RAY DIFFRACTIONf_chiral_restr0.034579
X-RAY DIFFRACTIONf_plane_restr0.005601
X-RAY DIFFRACTIONf_dihedral_angle_d13.1551305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6002-2.70430.31541390.347226562795
2.7043-2.82730.31341640.292526052769
2.8273-2.97640.31911530.256326372790
2.9764-3.16280.28021340.236926532787
3.1628-3.4070.27061360.231226742810
3.407-3.74970.24531350.205626792814
3.7497-4.2920.20371270.177127232850
4.292-5.40640.18791460.148527482894
5.4064-48.56070.21661480.174729183066
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)
10.98950.30871.44893.40562.93816.2183-0.1916-0.103-0.37490.52510.65390.37340.95760.356-0.35460.3322-0.0548-0.0740.32390.07340.3642171.9318-1.981924.2247
22.0673-1.037-1.42690.89450.86951.16090.42971.6198-0.0946-1.2225-0.2025-0.36120.2274-0.0975-0.23291.822-0.02490.17111.7909-0.20781.2598169.3943-24.4454-25.3376
39.75620.6741.73677.519-1.2444.3688-0.11970.27250.4995-0.2685-0.25830.0187-0.12960.36680.41660.7862-0.1182-0.14450.7065-0.19860.5276173.2203-15.2089-13.9259
41.1096-0.0776-1.27652.2471.32842.3902-0.03240.23660.2548-0.3232-0.1592-0.51330.04240.00130.36811.40180.72690.34551.29120.27731.9461189.92742.862211.6084
52.88951.29061.51293.50371.08153.79030.20840.8093-0.93170.17080.21430.02891.46380.6202-0.49061.07390.1018-0.12530.6727-0.1480.7193175.7965-22.51790.4429
61.54610.79080.91441.33632.6834.43110.01750.1355-0.3202-0.0808-0.04030.50380.65-0.21290.04110.5888-0.0265-0.21120.3626-0.03050.5614170.7961-7.997211.0493
73.2003-2.06550.60215.5741-0.47721.3614-0.1097-0.20580.02240.37690.125-0.07270.1265-0.1116-0.00840.28770.0013-0.01040.33080.04210.2519177.22899.926830.1381
84.4577-1.3121.2952.9396-0.50233.137-0.1696-0.47960.14120.33510.2149-0.0916-0.1952-0.1232-0.06420.39870.07090.02370.2849-0.09880.344171.647423.745832.1365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 27 through 62 )F0
2X-RAY DIFFRACTION2chain 'F' and (resid 63 through 73 )F0
3X-RAY DIFFRACTION3chain 'F' and (resid 74 through 101 )F0
4X-RAY DIFFRACTION4chain 'F' and (resid 105 through 107 )F0
5X-RAY DIFFRACTION5chain 'F' and (resid 137 through 216 )F0
6X-RAY DIFFRACTION6chain 'F' and (resid 217 through 331 )F0
7X-RAY DIFFRACTION7chain 'F' and (resid 332 through 416 )F0
8X-RAY DIFFRACTION8chain 'F' and (resid 417 through 506 )F0

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