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- PDB-9drq: Mumps virus fusion glycoprotein F stabilized in prefusion conformation -

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Basic information

Entry
Database: PDB / ID: 9drq
TitleMumps virus fusion glycoprotein F stabilized in prefusion conformation
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / Mumps virus / fusion protein / prefusion conformation / vaccine
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesMumps orthorubulavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsLai, Y.T. / Stewart-Jones, G.B.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structure-based design of glycoprotein subunit vaccines for mumps.
Authors: Loomis, R.J. / Lai, Y.T. / Sowers, S.B. / Fisher, B. / Derrien-Colemyn, A. / Ambrozak, D.R. / Tsybovsky, Y. / Crooke, S.N. / Latner, D.R. / Kong, W.P. / Ruckwardt, T.J. / Plotkin, S.A. / ...Authors: Loomis, R.J. / Lai, Y.T. / Sowers, S.B. / Fisher, B. / Derrien-Colemyn, A. / Ambrozak, D.R. / Tsybovsky, Y. / Crooke, S.N. / Latner, D.R. / Kong, W.P. / Ruckwardt, T.J. / Plotkin, S.A. / Kwong, P.D. / Mascola, J.R. / Graham, B.S. / Hickman, C.J. / Stewart-Jones, G.B.E.
History
DepositionSep 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2047
Polymers48,1461
Non-polymers2,0586
Water72140
1
A: Fusion glycoprotein F0
hetero molecules

A: Fusion glycoprotein F0
hetero molecules

A: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,61121
Polymers144,4383
Non-polymers6,17418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area24160 Å2
ΔGint-30 kcal/mol
Surface area57150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.823, 74.823, 460.854
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Fusion glycoprotein F0


Mass: 48145.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mumps orthorubulavirus / Production host: Homo sapiens (human) / References: UniProt: O91241
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M imidazole pH 8.0, 35% PEG1000, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 27169 / % possible obs: 99.8 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.035 / Rrim(I) all: 0.139 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.16-2.2426870.9961
2.24-2.3326800.8341
2.33-2.4326490.9221
2.43-2.5626990.9471
2.56-2.7226740.9721
2.72-2.9327010.9881
2.93-3.2327290.9931
3.23-3.6927140.9951
3.69-4.6527550.9941
4.65-5028810.9961

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→37.41 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 1359 5 %
Rwork0.2071 --
obs0.2091 27163 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 134 40 3542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073546
X-RAY DIFFRACTIONf_angle_d0.8684829
X-RAY DIFFRACTIONf_dihedral_angle_d16.4122192
X-RAY DIFFRACTIONf_chiral_restr0.058628
X-RAY DIFFRACTIONf_plane_restr0.005607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1665-2.24390.40271310.30772499X-RAY DIFFRACTION98
2.2439-2.33380.31481350.28442551X-RAY DIFFRACTION100
2.3338-2.43990.3391340.262530X-RAY DIFFRACTION100
2.4399-2.56860.33331350.24612573X-RAY DIFFRACTION100
2.5686-2.72940.28781330.24382542X-RAY DIFFRACTION100
2.7294-2.94010.35191350.24832562X-RAY DIFFRACTION100
2.9401-3.23580.27791370.23552592X-RAY DIFFRACTION100
3.2358-3.70370.23821360.20732592X-RAY DIFFRACTION100
3.7037-4.66490.20181380.17172619X-RAY DIFFRACTION99
4.6649-37.410.20741450.18812744X-RAY DIFFRACTION99
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)
1-0.00110.1523-0.08811.8541-1.03191.8561-0.0176-0.00450.03020.1737-0.0867-0.10570.09910.31810.12450.3230.0605-0.01240.4571-0.00470.3801-21.1259.6751.97
20.31770.2753-0.30230.4721-0.55292.831-0.0180.0063-0.05230.1302-0.0875-0.04610.00610.08690.10750.41920.0477-0.00660.41560.010.4448-25.93215.07255.175
31.25790.1220.58081.0495-0.22641.8981-0.10510.06430.2702-0.0034-0.0399-0.0006-0.32120.0910.15270.35680.0005-0.00150.39560.04810.3932-28.61435.93118.433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:148 )A0 - 148
2X-RAY DIFFRACTION2( CHAIN A AND RESID 149:271 )A149 - 271
3X-RAY DIFFRACTION3( CHAIN A AND RESID 272:456 )A272 - 456

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