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- PDB-5m1m: Crystal structure of matrix protein 1 from Influenza C virus (str... -

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Basic information

Entry
Database: PDB / ID: 5m1m
TitleCrystal structure of matrix protein 1 from Influenza C virus (strain C/Ann Arbor/1/1950)
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / influenza C / matrix protein 1
Function / homology
Function and homology information


viral capsid / channel activity / monoatomic ion transmembrane transport / structural constituent of virion / host cell endoplasmic reticulum membrane / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Influenza C virus M2 protein / Influenza C virus M1 protein / Influenza C virus M2 protein / Influenza C virus M1 protein
Similarity search - Domain/homology
Biological speciesInfluenza C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsRadzimanowski, J. / Weissenhorn, W.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Sci Rep / Year: 2017
Title: The Matrix protein M1 from influenza C virus induces tubular membrane invaginations in an in vitro cell membrane model.
Authors: Saletti, D. / Radzimanowski, J. / Effantin, G. / Midtvedt, D. / Mangenot, S. / Weissenhorn, W. / Bassereau, P. / Bally, M.
History
DepositionOct 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5263
Polymers17,4771
Non-polymers492
Water3,045169
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-17 kcal/mol
Surface area8130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.398, 26.841, 77.224
Angle α, β, γ (deg.)90.00, 108.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Matrix protein 1


Mass: 17477.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (strain C/Ann Arbor/1/1950)
Strain: C/Ann Arbor/1/1950 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6I7B9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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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: 1.87 Å3/Da / Density % sol: 34.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100mM Tris pH8.0, 200mM MgCl2 and25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93928 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93928 Å / Relative weight: 1
ReflectionResolution: 1.5→36.64 Å / Num. obs: 20888 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rsym value: 0.063 / Net I/σ(I): 12.1
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.527 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→31.502 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.42
RfactorNum. reflection% reflection
Rfree0.2195 1074 5.15 %
Rwork0.1878 --
obs0.1894 20868 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→31.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 2 169 1376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061195
X-RAY DIFFRACTIONf_angle_d0.9691601
X-RAY DIFFRACTIONf_dihedral_angle_d12.511468
X-RAY DIFFRACTIONf_chiral_restr0.068180
X-RAY DIFFRACTIONf_plane_restr0.005200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.56830.23641340.2252440X-RAY DIFFRACTION99
1.5683-1.6510.2621260.20962418X-RAY DIFFRACTION99
1.651-1.75440.27891470.21022458X-RAY DIFFRACTION100
1.7544-1.88980.25561310.19982490X-RAY DIFFRACTION99
1.8898-2.080.24681390.18962459X-RAY DIFFRACTION99
2.08-2.38090.2091230.17312491X-RAY DIFFRACTION99
2.3809-2.99930.20121330.18792498X-RAY DIFFRACTION99
2.9993-31.50890.19921410.17952540X-RAY DIFFRACTION98

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