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- PDB-8w3k: Crystal structure of prefusion-stabilized RSV F protein UFCR2-iSS-NQ -

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Basic information

Entry
Database: PDB / ID: 8w3k
TitleCrystal structure of prefusion-stabilized RSV F protein UFCR2-iSS-NQ
ComponentsPrefusion-stabilized RSV F protein UFCR2-iSS-NQ
KeywordsVIRAL PROTEIN / Respiratory syncytial virus / glycoprotein / prefusion vaccine / stabilized
Biological speciesHuman respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 UFCR2-iSS-NQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1216
Polymers55,6521
Non-polymers4695
Water1,928107
1
F: Prefusion-stabilized RSV F protein UFCR2-iSS-NQ
hetero molecules

F: Prefusion-stabilized RSV F protein UFCR2-iSS-NQ
hetero molecules

F: Prefusion-stabilized RSV F protein UFCR2-iSS-NQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,36318
Polymers166,9553
Non-polymers1,40815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_663z+1,x+1,y-21
crystal symmetry operation9_474y-1,z+2,x-11
Buried area13490 Å2
ΔGint3 kcal/mol
Surface area54360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.749, 168.749, 168.749
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 UFCR2-iSS-NQ


Mass: 55651.676 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.6 Å3/Da / Density % sol: 65.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M tri-Lithium citrate, 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: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→46.8 Å / Num. obs: 36826 / % possible obs: 99.81 % / Redundancy: 11.5 % / Biso Wilson estimate: 43.61 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.27
Reflection shellResolution: 2.3→2.384 Å / Num. unique obs: 3620 / CC1/2: 0.629

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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: 2.3→46.8 Å / SU ML: 0.3227 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2746 1808 4.91 %
Rwork0.2509 35018 -
obs0.2521 36826 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.82 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 30 107 3563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01073514
X-RAY DIFFRACTIONf_angle_d1.49684759
X-RAY DIFFRACTIONf_chiral_restr0.0877577
X-RAY DIFFRACTIONf_plane_restr0.0154600
X-RAY DIFFRACTIONf_dihedral_angle_d14.87271310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3311630.32522619X-RAY DIFFRACTION100
2.36-2.430.34151240.30832669X-RAY DIFFRACTION100
2.43-2.510.37161290.33832644X-RAY DIFFRACTION99.6
2.51-2.60.35251330.31122647X-RAY DIFFRACTION99.96
2.6-2.710.43461140.34562681X-RAY DIFFRACTION99.75
2.71-2.830.32761310.29872656X-RAY DIFFRACTION100
2.83-2.980.33431460.29362666X-RAY DIFFRACTION100
2.98-3.160.30781350.27762679X-RAY DIFFRACTION100
3.17-3.410.28561440.2772699X-RAY DIFFRACTION99.96
3.41-3.750.26511320.24922693X-RAY DIFFRACTION99.54
3.75-4.290.30691520.24932696X-RAY DIFFRACTION99.03
4.3-5.410.20491460.18992761X-RAY DIFFRACTION99.86
5.41-46.80.21141590.20192908X-RAY DIFFRACTION98.97

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