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- PDB-6s0y: Nanobody targeting influenza A matrix protein 2 ectodomain (M2e) -

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Basic information

Entry
Database: PDB / ID: 6s0y
TitleNanobody targeting influenza A matrix protein 2 ectodomain (M2e)
Components
  • M2e-VHH-23m
  • Matrix protein 2
KeywordsANTIVIRAL PROTEIN / Influenza A / Fc gamma Receptor IV / M2 matrix protein / nanobody
Function / homologyInfluenza virus matrix protein 2 / Influenza Matrix protein (M2) / proton transmembrane transporter activity / channel activity / host cell plasma membrane / virion membrane / membrane / Matrix protein 2
Function and homology information
Biological speciesLama glama (llama)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsVan Molle, I. / De Vlieger, D. / Schepens, B. / Remaut, H. / Saelens, X.
CitationJournal: Front Immunol / Year: 2019
Title: Selective Engagement of Fc gamma RIV by a M2e-Specific Single Domain Antibody Construct Protects Against Influenza A Virus Infection.
Authors: De Vlieger, D. / Hoffmann, K. / Van Molle, I. / Nerinckx, W. / Van Hoecke, L. / Ballegeer, M. / Creytens, S. / Remaut, H. / Hengel, H. / Schepens, B. / Saelens, X.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M2e-VHH-23m
B: M2e-VHH-23m
C: Matrix protein 2
D: Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)31,6294
Polymers31,6294
Non-polymers00
Water3,189177
1
A: M2e-VHH-23m
C: Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)15,8152
Polymers15,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area7290 Å2
MethodPISA
2
B: M2e-VHH-23m
D: Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)15,8152
Polymers15,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area7400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.470, 94.760, 53.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

21B-268-

HOH

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Components

#1: Antibody M2e-VHH-23m


Mass: 13171.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Matrix protein 2


Mass: 2642.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Influenza A virus (A/Jeju/2279/2007(H1N1)) / References: UniProt: B2VLW8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% ethanol, 10% PEG6000, 100 mM Na acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97965 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 1.8→53.06 Å / Num. obs: 27557 / % possible obs: 99.97 % / Redundancy: 13 % / CC1/2: 0.998 / Rpim(I) all: 0.044 / Χ2: 99.8 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1359 / CC1/2: 0.571 / Rpim(I) all: 0.666 / Χ2: 57.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGG

5hgg


Resolution: 1.81→47.38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.22 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22529 1254 4.6 %RANDOM
Rwork0.18693 ---
obs0.18872 25859 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2---0.96 Å20 Å2
3----0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.81→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 0 177 2193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132047
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181834
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.6482763
X-RAY DIFFRACTIONr_angle_other_deg1.4361.5864231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2435261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.43320.734109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7915318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9411518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6462.7281060
X-RAY DIFFRACTIONr_mcbond_other2.6282.7271059
X-RAY DIFFRACTIONr_mcangle_it3.9664.0551314
X-RAY DIFFRACTIONr_mcangle_other3.9654.0551315
X-RAY DIFFRACTIONr_scbond_it3.5163.122987
X-RAY DIFFRACTIONr_scbond_other3.5153.122987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5424.5121449
X-RAY DIFFRACTIONr_long_range_B_refined7.24530.5362171
X-RAY DIFFRACTIONr_long_range_B_other7.24430.5342171
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 86 -
Rwork0.292 1901 -
obs--100 %

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