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- PDB-4n8c: Three-dimensional structure of the extracellular domain of Matrix... -

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Basic information

Entry
Database: PDB / ID: 4n8c
TitleThree-dimensional structure of the extracellular domain of Matrix protein 2 of influenza A virus
Components
  • Extracellular domain of influenza Matrix protein 2
  • Heavy chain of monoclonal antibody
  • Light chain of monoclonal antibody
KeywordsIMMUNE SYSTEM / Antibody-peptide complex / Influenza A virus protein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsCho, K.J. / Seok, J.H. / Kim, S. / Roose, K. / Schepens, B. / Fiers, W. / Saelens, X. / Kim, K.H.
CitationJournal: J.Virol. / Year: 2015
Title: Structure of the extracellular domain of matrix protein 2 of influenza A virus in complex with a protective monoclonal antibody
Authors: Cho, K.J. / Schepens, B. / Seok, J.H. / Kim, S. / Roose, K. / Lee, J.H. / Gallardo, R. / Hamme, E.V. / Schymkowitz, J. / Rousseau, F. / Fiers, W. / Saelens, X. / Kim, K.H.
History
DepositionOct 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 2023Group: 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 1.4Oct 30, 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
H: Heavy chain of monoclonal antibody
I: Heavy chain of monoclonal antibody
L: Light chain of monoclonal antibody
M: Light chain of monoclonal antibody
X: Extracellular domain of influenza Matrix protein 2
Y: Extracellular domain of influenza Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)101,8176
Polymers101,8176
Non-polymers00
Water12,448691
1
H: Heavy chain of monoclonal antibody
L: Light chain of monoclonal antibody
X: Extracellular domain of influenza Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)50,9093
Polymers50,9093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-29 kcal/mol
Surface area20320 Å2
MethodPISA
2
I: Heavy chain of monoclonal antibody
M: Light chain of monoclonal antibody
Y: Extracellular domain of influenza Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)50,9093
Polymers50,9093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-32 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.353, 72.276, 78.446
Angle α, β, γ (deg.)86.880, 77.530, 84.630
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Heavy chain of monoclonal antibody


Mass: 23861.680 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: 24404.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Extracellular domain of influenza Matrix protein 2


Mass: 2642.940 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in influenza A virus
Source: (synth.) Influenza A virus (A/Puerto Rico/8/1934(H1N1))
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.18 Å3/Da / Density % sol: 43.66 % / Mosaicity: 0.296 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG3350, 200 mM Sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 113047 / Num. obs: 109543 / % possible obs: 96.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.054 / Χ2: 0.983 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.663.90.674107390.73195.2
1.66-1.7240.479108140.812195.6
1.72-1.840.315108580.901196.1
1.8-1.940.213108991.003196.3
1.9-2.0240.137109801.054196.8
2.02-2.1740.092109181.08197.1
2.17-2.393.90.072110771.017197.7
2.39-2.743.90.053110531.068198
2.74-3.453.90.039111610.973198.5
3.45-503.80.035110441.183197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBM

3gbm


Resolution: 1.6→38.43 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.204 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 5494 5 %RANDOM
Rwork0.1932 ---
obs0.1957 104049 96.58 %-
all-107733 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.44 Å2 / Biso mean: 27.2785 Å2 / Biso min: 10.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å2-0.56 Å20.04 Å2
2---0.67 Å20.42 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7005 0 0 691 7696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.027284
X-RAY DIFFRACTIONr_bond_other_d0.0060.026599
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.9449942
X-RAY DIFFRACTIONr_angle_other_deg1.305315303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3625931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85824.375288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.813151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7161528
X-RAY DIFFRACTIONr_chiral_restr0.1240.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218302
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021638
LS refinement shellResolution: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 378 -
Rwork0.321 7217 -
all-7595 -
obs--91 %

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