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- PDB-5dlm: Complex of Influenza M2e and Antibody -

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Basic information

Entry
Database: PDB / ID: 5dlm
TitleComplex of Influenza M2e and Antibody
Components
  • Heavy chain of monoclonal antibody
  • Light chain of monoclonal antibody
  • Matrix protein 2
KeywordsIMMUNE SYSTEM / Complex / Antibody / Extracellular domain
Function / homology
Function and homology information


uncoating of virus / Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis ...uncoating of virus / Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / suppression by virus of host autophagy / protein complex oligomerization / monoatomic ion channel activity / proton transmembrane transporter activity / Viral mRNA Translation / symbiont genome entry into host cell via pore formation in plasma membrane / host cell plasma membrane / virion membrane / extracellular region / membrane / plasma membrane
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Matrix protein 2 / Matrix protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCho, K.J. / Schepens, B. / Moonens, K. / Deng, L. / Fiers, W. / Remaut, H. / Saelens, X.
Funding support Belgium, China, 5items
OrganizationGrant numberCountry
Fonds Wetenschappelijk Onderzoek3G052412N Belgium
Fonds Wetenschappelijk Onderzoek - Vlaanderen Belgium
China Scholarship Council2011674067 China
VIBIUAP BELVIR project p7/45 Belgium
Ghent UniversityBOF12/GOA/014 Belgium
CitationJournal: J.Virol. / Year: 2015
Title: Crystal Structure of the Conserved Amino Terminus of the Extracellular Domain of Matrix Protein 2 of Influenza A Virus Gripped by an Antibody.
Authors: Cho, K.J. / Schepens, B. / Moonens, K. / Deng, L. / Fiers, W. / Remaut, H. / Saelens, X.
History
DepositionSep 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy chain of monoclonal antibody
L: Light chain of monoclonal antibody
I: Heavy chain of monoclonal antibody
M: Light chain of monoclonal antibody
X: Matrix protein 2
Y: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2408
Polymers99,0486
Non-polymers1922
Water5,495305
1
H: Heavy chain of monoclonal antibody
L: Light chain of monoclonal antibody
X: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6204
Polymers49,5243
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-44 kcal/mol
Surface area19540 Å2
MethodPISA
2
I: Heavy chain of monoclonal antibody
M: Light chain of monoclonal antibody
Y: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6204
Polymers49,5243
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-45 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.640, 101.440, 212.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Heavy chain of monoclonal antibody


Mass: 23017.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Light chain of monoclonal antibody


Mass: 24008.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Matrix protein 2


Mass: 2497.675 Da / Num. of mol.: 2 / Mutation: Trp15Gly / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: A4U6V3, UniProt: P06821*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM sodium acetate (pH 5.0), 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 50230 / % possible obs: 97.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.5 / % possible all: 84.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DVB

4dvb


Resolution: 2.2→49.21 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 13.277 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 2494 5 %RANDOM
Rwork0.1866 ---
obs0.1893 47639 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.57 Å2 / Biso mean: 46.022 Å2 / Biso min: 23.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.2→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6727 0 10 305 7042
Biso mean--72.47 42.27 -
Num. residues----882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.026924
X-RAY DIFFRACTIONr_bond_other_d0.0080.026343
X-RAY DIFFRACTIONr_angle_refined_deg2.2641.9539422
X-RAY DIFFRACTIONr_angle_other_deg1.58314711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7115882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95523.822259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.129151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0741531
X-RAY DIFFRACTIONr_chiral_restr0.1360.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217725
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021526
X-RAY DIFFRACTIONr_mcbond_it1.9372.7733531
X-RAY DIFFRACTIONr_mcbond_other1.9372.7733530
X-RAY DIFFRACTIONr_mcangle_it2.944.1524406
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.577 152 -
Rwork0.579 3086 -
all-3238 -
obs--87.02 %
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)
12.5849-1.0851-1.1741.64160.24472.5073-0.1918-0.2490.03110.07740.0323-0.02390.27450.23290.15940.04380.0154-0.0030.07290.00580.062726.652-10.98245.13
212.4321-0.39168.5392.77431.470115.9179-0.16620.1235-0.4531-0.419-0.05120.51920.1952-1.11760.21740.3003-0.1001-0.050.1970.00120.2728-11.649-3.55135.793
33.27511.42091.9061.45751.29613.2254-0.07470.05010.02440.03880.02440.15080.1774-0.15170.05030.0295-0.02250.02260.0221-0.00890.0816-2.3-7.20639.654
42.9522-0.77010.15313.7140.00854.4444-0.12310.3750.0017-0.63510.0334-0.0070.39730.21960.08970.2568-0.0603-0.00140.1188-0.0040.028114.69121.8586.296
51.7603-1.6041-0.54286.5089-0.2841.5469-0.08260.16320.3535-0.33580.0480.0621-0.0878-0.00870.03460.1482-0.0727-0.06670.13750.05660.13411.17538.31112.023
62.21660.7398-0.24396.6221.79813.07880.09360.09130.6137-0.435-0.07680.2588-0.37520.0841-0.01670.1707-0.0204-0.0160.11190.08760.213212.88252.84713.524
711.60383.03794.2751.64541.33844.06660.07740.347-0.1286-0.09390.0172-0.13140.08120.0967-0.09460.08890.01250.05370.06420.03350.117630.393-9.26619.822
83.3786-0.23330.49542.00690.51232.9419-0.03980.3712-0.424-0.1675-0.03860.04430.23440.04630.07840.06110.0030.04360.0555-0.01570.136328.08-16.48724.506
92.9988-1.6348-1.88752.81851.68543.79740.1360.31240.0833-0.2718-0.07630.1317-0.3715-0.3262-0.05980.0616-0.0071-0.01770.09610.02960.0698-4.5062.89526.652
103.04553.9251.50837.55752.9733.1926-0.03260.003-0.2185-0.0068-0.0141-0.04810.1512-0.08550.04670.0472-0.04030.03180.08040.00680.076411.37719.40632.379
112.32390.95870.74033.53220.88532.45370.0003-0.0935-0.06880.0418-0.0318-0.19050.16880.04820.03140.0381-0.0180.01130.03380.00670.029918.74521.72228.127
123.556-1.23381.29262.5753-1.66763.3785-0.0749-0.07310.80950.2260.05310.1365-0.5589-0.21820.02180.2001-0.02450.03320.0574-0.00160.40742.45555.71126.118
137.7617-2.5577-0.114910.2594-3.621314.34530.04150.06750.12870.05390.0497-0.68560.22271.3887-0.09120.14640.07010.05080.20380.02690.152838.658-19.73437.005
147.7418-0.07780.89977.43715.016910.78750.25930.1047-0.5664-0.1506-0.2260.08351.399-0.0656-0.03330.45130.04790.04930.17010.03580.164821.34510.82515.609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 120
2X-RAY DIFFRACTION2H121 - 135
3X-RAY DIFFRACTION3H136 - 216
4X-RAY DIFFRACTION4I2 - 85
5X-RAY DIFFRACTION5I86 - 135
6X-RAY DIFFRACTION6I136 - 215
7X-RAY DIFFRACTION7L1 - 31
8X-RAY DIFFRACTION8L32 - 110
9X-RAY DIFFRACTION9L111 - 217
10X-RAY DIFFRACTION10M1 - 32
11X-RAY DIFFRACTION11M33 - 110
12X-RAY DIFFRACTION12M111 - 217
13X-RAY DIFFRACTION13X2 - 10
14X-RAY DIFFRACTION14Y2 - 10

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