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- PDB-8w3e: Crystal structure of prefusion-stabilized RSV F protein UFCR1 -

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Basic information

Entry
Database: PDB / ID: 8w3e
TitleCrystal structure of prefusion-stabilized RSV F protein UFCR1
ComponentsPrefusion-stabilized RSV F protein UFCR1
KeywordsVIRAL PROTEIN / Respiratory syncytial virus / glycoprotein / prefusion vaccine / stabilized
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHuman respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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 UFCR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1024
Polymers55,7131
Non-polymers3893
Water2,180121
1
F: Prefusion-stabilized RSV F protein UFCR1
hetero molecules

F: Prefusion-stabilized RSV F protein UFCR1
hetero molecules

F: Prefusion-stabilized RSV F protein UFCR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,30612
Polymers167,1383
Non-polymers1,1689
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 area13040 Å2
ΔGint-8 kcal/mol
Surface area55430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.033, 170.033, 170.033
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 UFCR1


Mass: 55712.688 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.68 Å3/Da / Density % sol: 66.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-Sodium tartrate, 18% 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: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.26→36.25 Å / Num. obs: 39817 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 70.8 % / Biso Wilson estimate: 44.35 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1807 / Rpim(I) all: 0.022 / Rrim(I) all: 0.182 / Net I/σ(I): 27.5
Reflection shellResolution: 2.26→2.34 Å / Rmerge(I) obs: 0.181 / Num. unique obs: 39803 / CC1/2: 1 / Rpim(I) all: 0.0215

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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: 2.26→36.25 Å / SU ML: 0.2845 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 1961 4.93 %
Rwork0.227 37856 -
obs0.2283 39817 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.24 Å2
Refinement stepCycle: LAST / Resolution: 2.26→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 25 121 3573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01053506
X-RAY DIFFRACTIONf_angle_d1.54694751
X-RAY DIFFRACTIONf_chiral_restr0.0862576
X-RAY DIFFRACTIONf_plane_restr0.0161598
X-RAY DIFFRACTIONf_dihedral_angle_d14.99931305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.320.36411280.32412675X-RAY DIFFRACTION100
2.32-2.380.29531470.28072635X-RAY DIFFRACTION100
2.38-2.450.27261100.28082684X-RAY DIFFRACTION100
2.45-2.530.31111270.28122662X-RAY DIFFRACTION100
2.53-2.620.31651430.27572662X-RAY DIFFRACTION100
2.62-2.720.34651530.28162647X-RAY DIFFRACTION100
2.72-2.850.35841450.27932656X-RAY DIFFRACTION99.96
2.85-30.28841250.28312713X-RAY DIFFRACTION99.96
3-3.180.2841410.25152671X-RAY DIFFRACTION99.93
3.19-3.430.25151280.24372721X-RAY DIFFRACTION99.89
3.43-3.770.24021580.21532699X-RAY DIFFRACTION99.97
3.78-4.320.21911530.20042724X-RAY DIFFRACTION99.97
4.32-5.440.23271640.17842763X-RAY DIFFRACTION99.93
5.44-36.250.20021390.19722944X-RAY DIFFRACTION99.39

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