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- PDB-8w3q: Crystal structure of prefusion-stabilized hMPV F protein UFCM1-P2-iSS -

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Basic information

Entry
Database: PDB / ID: 8w3q
TitleCrystal structure of prefusion-stabilized hMPV F protein UFCM1-P2-iSS
Componentsprefusion-stabilized hMPV F protein UFCM1-P2-iSS
KeywordsVIRAL PROTEIN / Respiratory syncytial virus / glycoprotein / prefusion vaccine / stabilized
Biological specieshuman metapneumovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.99 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 hMPV F protein UFCM1-P2-iSS


Theoretical massNumber of molelcules
Total (without water)55,7501
Polymers55,7501
Non-polymers00
Water00
1
F: prefusion-stabilized hMPV F protein UFCM1-P2-iSS

F: prefusion-stabilized hMPV F protein UFCM1-P2-iSS

F: prefusion-stabilized hMPV F protein UFCM1-P2-iSS


Theoretical massNumber of molelcules
Total (without water)167,2513
Polymers167,2513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Buried area9010 Å2
ΔGint-33 kcal/mol
Surface area56000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.745, 185.745, 185.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2

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Components

#1: Protein prefusion-stabilized hMPV F protein UFCM1-P2-iSS


Mass: 55750.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human metapneumovirus / Production host: Cricetulus griseus (Chinese hamster)
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: 4.79 Å3/Da / Density % sol: 74.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.4M potassium dihydrogen phosphate, 1.2M sodium dihydrogen phosphate, 0.1M phosphate-citrate pH4.37

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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: Sep 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 5.99→49.64 Å / Num. obs: 2793 / % possible obs: 99.57 % / Redundancy: 38.2 % / Biso Wilson estimate: 308.05 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.42
Reflection shellResolution: 5.99→6.215 Å / Num. unique obs: 278 / CC1/2: 0.728

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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: 5.99→49.64 Å / SU ML: 0.5699 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3546 131 4.69 %
Rwork0.2237 2662 -
obs0.23 2793 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 252.07 Å2
Refinement stepCycle: LAST / Resolution: 5.99→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 0 0 3149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01753191
X-RAY DIFFRACTIONf_angle_d2.37994322
X-RAY DIFFRACTIONf_chiral_restr0.1048517
X-RAY DIFFRACTIONf_plane_restr0.026553
X-RAY DIFFRACTIONf_dihedral_angle_d13.66221174
LS refinement shellResolution: 5.99→49.64 Å
RfactorNum. reflection% reflection
Rfree0.3546 131 -
Rwork0.2237 2662 -
obs--99.89 %

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