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- PDB-7sej: Structure-based design of prefusion-stabilized human metapneumovi... -

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Basic information

Entry
Database: PDB / ID: 7sej
TitleStructure-based design of prefusion-stabilized human metapneumovirus fusion proteins
Components
  • Fusion glycoprotein F1 subunit
  • Fusion glycoprotein F2 subunit
KeywordsVIRAL PROTEIN / human metapneumovirus / fusion protein
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHuman metapneumovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsHsieh, C.-L. / Rush, S.A. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Robert A. Welch FoundationF-0003-19620604 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins.
Authors: Hsieh, C.L. / Rush, S.A. / Palomo, C. / Chou, C.W. / Pickens, W. / Mas, V. / McLellan, J.S.
History
DepositionSep 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fusion glycoprotein F2 subunit
F: Fusion glycoprotein F1 subunit
C: Fusion glycoprotein F2 subunit
A: Fusion glycoprotein F1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,8298
Polymers120,9444
Non-polymers8854
Water2,450136
1
B: Fusion glycoprotein F2 subunit
F: Fusion glycoprotein F1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9144
Polymers60,4722
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-47 kcal/mol
Surface area20800 Å2
MethodPISA
2
C: Fusion glycoprotein F2 subunit
A: Fusion glycoprotein F1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9144
Polymers60,4722
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-49 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.379, 105.809, 90.990
Angle α, β, γ (deg.)90.000, 105.260, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fusion glycoprotein F2 subunit


Mass: 11015.444 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: H6X1Z0
#2: Protein Fusion glycoprotein F1 subunit


Mass: 49456.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the protein is cleaved into the two subunits (entities 1 and 2) as it transported through ER-Golgi
Source: (gene. exp.) Human metapneumovirus / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: H6X1Z0
#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.: 4 / 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.: 136 / 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: 2.43 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 500 nl of hMPV F (10 mg/ml) with 500 nl of reservoir solution containing 0.1 M MES pH 6.0 and 12%(v/v) PEK 20k.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→45.4 Å / Num. obs: 35650 / % possible obs: 97.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 40.37 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.073 / Net I/σ(I): 8.3
Reflection shellResolution: 2.51→2.6 Å / Rmerge(I) obs: 0.038 / Mean I/σ(I) obs: 15.5 / Num. unique obs: 801 / CC1/2: 0.994 / Rpim(I) all: 0.037

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wb0

5wb0


Resolution: 2.51→45.31 Å / SU ML: 0.3247 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2527 1802 5.06 %
Rwork0.209 33814 -
obs0.2113 35616 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.77 Å2
Refinement stepCycle: LAST / Resolution: 2.51→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6562 0 56 136 6754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526707
X-RAY DIFFRACTIONf_angle_d0.70019073
X-RAY DIFFRACTIONf_chiral_restr0.04731088
X-RAY DIFFRACTIONf_plane_restr0.0061155
X-RAY DIFFRACTIONf_dihedral_angle_d23.04472470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.580.30861580.26242576X-RAY DIFFRACTION98.03
2.58-2.650.33331650.25772608X-RAY DIFFRACTION98.33
2.65-2.740.2831200.23732612X-RAY DIFFRACTION98.03
2.74-2.840.31591130.24172587X-RAY DIFFRACTION96.77
2.84-2.950.31431200.2522561X-RAY DIFFRACTION94.63
2.95-3.080.2841220.26142625X-RAY DIFFRACTION98.39
3.08-3.250.29011660.2372633X-RAY DIFFRACTION98.59
3.25-3.450.30051510.21982562X-RAY DIFFRACTION97.31
3.45-3.720.2481250.21432545X-RAY DIFFRACTION95.46
3.72-4.090.23391420.20032631X-RAY DIFFRACTION98.58
4.09-4.680.20781240.17452602X-RAY DIFFRACTION96.98
4.68-5.90.23441350.18152652X-RAY DIFFRACTION97.65
5.9-45.310.18721610.17482620X-RAY DIFFRACTION96.8

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