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- PDB-7m0i: Crystal structure of a human metapneumovirus subtype B2 trimeric ... -

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Basic information

Entry
Database: PDB / ID: 7m0i
TitleCrystal structure of a human metapneumovirus subtype B2 trimeric fusion protein
Components
  • Fusion glycoprotein F1
  • Fusion glycoprotein F2
KeywordsVIRAL PROTEIN
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / membrane => GO:0016020 / 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: 2.81 Å
AuthorsHuang, J. / Mousa, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI14386 United States
CitationJournal: J.Virol. / Year: 2021
Title: Structure, Immunogenicity, and Conformation-Dependent Receptor Binding of the Postfusion Human Metapneumovirus F Protein.
Authors: Huang, J. / Chopra, P. / Liu, L. / Nagy, T. / Murray, J. / Tripp, R.A. / Boons, G.J. / Mousa, J.J.
History
DepositionMar 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Fusion glycoprotein F2
H: Fusion glycoprotein F1
I: Fusion glycoprotein F2
J: Fusion glycoprotein F1
K: Fusion glycoprotein F2
L: Fusion glycoprotein F1
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1
C: Fusion glycoprotein F2
D: Fusion glycoprotein F1
E: Fusion glycoprotein F2
F: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,03830
Polymers342,05612
Non-polymers3,98218
Water45025
1
G: Fusion glycoprotein F2
H: Fusion glycoprotein F1
I: Fusion glycoprotein F2
J: Fusion glycoprotein F1
K: Fusion glycoprotein F2
L: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,01915
Polymers171,0286
Non-polymers1,9919
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51210 Å2
ΔGint-347 kcal/mol
Surface area51980 Å2
MethodPISA
2
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1
C: Fusion glycoprotein F2
D: Fusion glycoprotein F1
E: Fusion glycoprotein F2
F: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,01915
Polymers171,0286
Non-polymers1,9919
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50900 Å2
ΔGint-343 kcal/mol
Surface area52780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.530, 128.100, 431.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Fusion glycoprotein F2


Mass: 10195.467 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus / Production host: Homo sapiens (human) / References: UniProt: C6F474
#2: Protein
Fusion glycoprotein F1


Mass: 46813.914 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus / Production host: Homo sapiens (human) / References: UniProt: C6F474
#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.: 18 / 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.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailshMPV F is a class I fusion glycoprotein, synthesized as an inactive precursor (F0) that needs to be ...hMPV F is a class I fusion glycoprotein, synthesized as an inactive precursor (F0) that needs to be cleaved to become fusion competent. Proteolytic cleavage generates two disulfide-linked subunits (F2 N-terminal and F1 C-terminal fragments) that assemble into a homotrimer. Specifically, REEQIENPRQSKKRKRR at the C-terminus of Fusion glycoprotein F2 is cleaved after trypsin treatment. VATAAAVTAGIAIAKTIR at the N-terminus of Fusion glycoprotein F1 and KGNTSGRENLYFQGGGGGSGYIPEAPRDQAYVRKDGEWVLLSTFLGGTEGR at the C-terminus of Fusion glycoprotein F1 are cleaved after trypsin treatment.

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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: 4.63 Å3/Da / Density % sol: 73.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.81→49.69 Å / Num. obs: 155097 / % possible obs: 75.6 % / Redundancy: 14.9 % / Biso Wilson estimate: 34.4 Å2 / CC1/2: 0.973 / CC star: 0.993 / Net I/σ(I): 6.5
Reflection shellResolution: 2.811→2.911 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 0.77 / Num. unique obs: 1294 / CC1/2: 0.227

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L1X

5l1x


Resolution: 2.81→49.69 Å / SU ML: 0.3906 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2908 5879 5.01 %
Rwork0.2539 111421 -
obs0.2558 117300 75.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.29 Å2
Refinement stepCycle: LAST / Resolution: 2.81→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19279 0 252 25 19556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012819818
X-RAY DIFFRACTIONf_angle_d1.763926886
X-RAY DIFFRACTIONf_chiral_restr0.10383228
X-RAY DIFFRACTIONf_plane_restr0.01163451
X-RAY DIFFRACTIONf_dihedral_angle_d19.46687273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.840.275590.3426179X-RAY DIFFRACTION3.68
2.84-2.870.3078220.3449348X-RAY DIFFRACTION7.27
2.87-2.910.4217330.3679675X-RAY DIFFRACTION13.84
2.91-2.950.4454520.3956844X-RAY DIFFRACTION17.54
2.95-2.990.327640.36551279X-RAY DIFFRACTION26.18
2.99-3.030.427790.36211729X-RAY DIFFRACTION35.4
3.03-3.070.34941150.35182216X-RAY DIFFRACTION45.68
3.07-3.120.37071210.35842597X-RAY DIFFRACTION52.79
3.12-3.160.35321450.34222926X-RAY DIFFRACTION60.32
3.16-3.220.34911690.32763257X-RAY DIFFRACTION66.55
3.22-3.270.34541880.31313590X-RAY DIFFRACTION73.47
3.27-3.330.35512170.31163804X-RAY DIFFRACTION79.37
3.33-3.40.36392030.30074262X-RAY DIFFRACTION86.23
3.4-3.460.34572500.31254559X-RAY DIFFRACTION92.82
3.46-3.540.32632460.29464791X-RAY DIFFRACTION99.06
3.54-3.620.29982660.28964864X-RAY DIFFRACTION99.94
3.62-3.710.33052660.28064911X-RAY DIFFRACTION99.94
3.71-3.810.32182600.26664911X-RAY DIFFRACTION99.9
3.81-3.920.32062690.26314870X-RAY DIFFRACTION99.98
3.92-4.050.29912630.25114887X-RAY DIFFRACTION99.96
4.05-4.20.30712500.23444925X-RAY DIFFRACTION99.94
4.2-4.360.24512580.21494927X-RAY DIFFRACTION99.92
4.36-4.560.24542350.20324958X-RAY DIFFRACTION99.83
4.56-4.80.24522500.20474928X-RAY DIFFRACTION99.92
4.8-5.10.22222550.20194953X-RAY DIFFRACTION99.87
5.1-5.50.26342770.20964940X-RAY DIFFRACTION99.92
5.5-6.050.25542630.22914978X-RAY DIFFRACTION99.94
6.05-6.920.25322790.22744995X-RAY DIFFRACTION99.94
6.92-8.710.23922970.20795042X-RAY DIFFRACTION99.93
8.72-49.690.23522780.21145276X-RAY DIFFRACTION99.8

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