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- PDB-8w3o: Crystal structure of prefusion-stabilized RSV F protein UFCR3-GDQ -

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Entry
Database: PDB / ID: 8w3o
TitleCrystal structure of prefusion-stabilized RSV F protein UFCR3-GDQ
Componentsprefusion-stabilized RSV F protein UFCR3-GDQ
KeywordsVIRAL PROTEIN / Respiratory syncytial virus / glycoprotein / prefusion vaccine / stabilized
Biological speciesHuman respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsLee, Y.Z. / Stanfield, R.L. / Wilson, I.A. / Zhu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2024
Title: Rational design of uncleaved prefusion-closed trimer vaccines for human respiratory syncytial virus and metapneumovirus.
Authors: Lee, Y.Z. / Han, J. / Zhang, Y.N. / Ward, G. / Braz Gomes, K. / Auclair, S. / Stanfield, R.L. / He, L. / Wilson, I.A. / Zhu, J.
History
DepositionFeb 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: prefusion-stabilized RSV F protein UFCR3-GDQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2252
Polymers56,0041
Non-polymers2211
Water3,027168
1
F: prefusion-stabilized RSV F protein UFCR3-GDQ
hetero molecules

F: prefusion-stabilized RSV F protein UFCR3-GDQ
hetero molecules

F: prefusion-stabilized RSV F protein UFCR3-GDQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,6766
Polymers168,0123
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12230 Å2
ΔGint-32 kcal/mol
Surface area55300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.529, 169.529, 169.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4

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Components

#1: Protein prefusion-stabilized RSV F protein UFCR3-GDQ


Mass: 56003.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Production host: Cricetulus griseus (Chinese hamster)
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.62 Å3/Da / Density % sol: 66.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium thiocyanate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.31→41.12 Å / Num. obs: 36949 / % possible obs: 99.3 % / Redundancy: 1 % / Biso Wilson estimate: 30.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1368 / Net I/σ(I): 31.5
Reflection shellResolution: 2.31→2.393 Å / Num. unique obs: 3420 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→41.12 Å / SU ML: 0.2092 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 1814 4.91 %
Rwork0.2006 35135 -
obs0.202 36949 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.66 Å2
Refinement stepCycle: LAST / Resolution: 2.31→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 14 168 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863534
X-RAY DIFFRACTIONf_angle_d1.04484795
X-RAY DIFFRACTIONf_chiral_restr0.061579
X-RAY DIFFRACTIONf_plane_restr0.0066607
X-RAY DIFFRACTIONf_dihedral_angle_d16.08081318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.24741560.21522472X-RAY DIFFRACTION93.56
2.37-2.440.2421280.20532593X-RAY DIFFRACTION97.6
2.44-2.520.23911230.22092690X-RAY DIFFRACTION99.89
2.52-2.610.3271330.23012688X-RAY DIFFRACTION100
2.61-2.710.30171190.22182670X-RAY DIFFRACTION100
2.71-2.830.28291310.23142706X-RAY DIFFRACTION100
2.83-2.980.2521430.23052683X-RAY DIFFRACTION100
2.98-3.170.27691390.22052705X-RAY DIFFRACTION100
3.17-3.420.22131410.21812720X-RAY DIFFRACTION100
3.42-3.760.2411390.1912732X-RAY DIFFRACTION100
3.76-4.30.19731540.17962734X-RAY DIFFRACTION100
4.3-5.420.1681480.16122789X-RAY DIFFRACTION100
5.42-41.120.21741600.19632953X-RAY DIFFRACTION99.71

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