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- PDB-8t9z: Structural of M8C10 Fab in complex human metapneumovirus fusion p... -

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Basic information

Entry
Database: PDB / ID: 8t9z
TitleStructural of M8C10 Fab in complex human metapneumovirus fusion protein
Components
  • Fusion glycoprotein F0
  • M8C10 Fab Heavy Chain
  • M8C10 Fab Light Chain
KeywordsVIRAL PROTEIN/Immune System / Neutralizing antibody / respiratory / metapneumovirus / fusion / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.995 Å
AuthorsSu, H.P. / Eddins, M.J. / Shipman, J.M. / Kostas, J. / Reid, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Virol. / Year: 2023
Title: Structural characterization of M8C10, a neutralizing antibody targeting a highly conserved prefusion-specific epitope on the metapneumovirus fusion trimerization interface.
Authors: Xiao, X. / Wen, Z. / Chen, Q. / Shipman, J.M. / Kostas, J. / Reid, J.C. / Warren, C. / Tang, A. / Luo, B. / O'Donnell, G. / Fridman, A. / Chen, Z. / Vora, K.A. / Zhang, L. / Su, H.-P. / Eddins, M.J.
History
DepositionJun 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F0
H: M8C10 Fab Heavy Chain
L: M8C10 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)100,1263
Polymers100,1263
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.900, 117.670, 181.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Fusion glycoprotein F0


Mass: 51747.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: G3KCK8
#2: Antibody M8C10 Fab Heavy Chain


Mass: 24736.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody M8C10 Fab Light Chain


Mass: 23641.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350, 200 mM Sodium Iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→49.35 Å / Num. obs: 21582 / % possible obs: 99.54 % / Redundancy: 6 % / Biso Wilson estimate: 67.73 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.073 / Rrim(I) all: 0.178 / Net I/σ(I): 8.3
Reflection shellResolution: 2.99→3.13 Å / Num. unique obs: 2511 / CC1/2: 0.762

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.995→49.345 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2803 1133 5.25 %
Rwork0.2435 20449 -
obs0.2455 21582 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.62 Å2 / Biso mean: 72.4035 Å2 / Biso min: 34.14 Å2
Refinement stepCycle: final / Resolution: 2.995→49.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 0 26 6142
Biso mean---53.96 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046236
X-RAY DIFFRACTIONf_angle_d0.7418481
X-RAY DIFFRACTIONf_chiral_restr0.045989
X-RAY DIFFRACTIONf_plane_restr0.0041082
X-RAY DIFFRACTIONf_dihedral_angle_d3.1533727
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.995-3.1310.39141610.34412511100
3.131-3.29610.34411300.29342541100
3.2961-3.50250.32631550.28092503100
3.5025-3.77290.30891240.26262535100
3.7729-4.15240.31681360.24992556100
4.1524-4.75280.24111390.2141256299
4.7528-5.98640.23841420.228256599
5.9864-49.30.24581460.2146267699

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