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- PDB-5v8a: Crystal structure of Influenza A virus matrix protein M1 (NLS-88R... -

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Basic information

Entry
Database: PDB / ID: 5v8a
TitleCrystal structure of Influenza A virus matrix protein M1 (NLS-88R, pH 7.3)
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / Influenza A / Matrix protein / NLS-88R mutant / pH 7.3
Function / homology
Function and homology information


viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / membrane
Similarity search - Function
Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix protein M1, N-terminal subdomain 2 / Influenza Virus Matrix Protein; Chain A, domain 1 / Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) ...Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix protein M1, N-terminal subdomain 2 / Influenza Virus Matrix Protein; Chain A, domain 1 / Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMusayev, F.N. / Safo, M.K. / Desai, U.R. / Xie, H. / Mosier, P.D. / Zhou, Q. / Chiang, M.-J. / Kosikova, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA16059 United States
Center for Biologics Evaluation and Research (CBER)/FDA United States
CitationJournal: Emerg Microbes Infect / Year: 2017
Title: Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication.
Authors: Chiang, M.J. / Musayev, F.N. / Kosikova, M. / Lin, Z. / Gao, Y. / Mosier, P.D. / Althufairi, B. / Ye, Z. / Zhou, Q. / Desai, U.R. / Xie, H. / Safo, M.K.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)19,0981
Polymers19,0981
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.664, 33.341, 36.151
Angle α, β, γ (deg.)112.18, 100.38, 94.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Matrix protein 1 / M1


Mass: 19098.055 Da / Num. of mol.: 1 / Mutation: G88R, R101S, R105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1)
Strain: A/Wilson-Smith/1933 H1N1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Nico21 (DE3) / References: UniProt: P05777
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.57 Å3/Da / Density % sol: 21.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: Protein solution: 10 mg/ml in K2HPO4/KH2PO4, 0.2M NaCl, 10bME, pH 7.2. Reservoir solution: 0.2M NaF, 20% PEG-3350, pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 3→28.7 Å / Num. obs: 2187 / % possible obs: 94.5 % / Redundancy: 2.83 % / Biso Wilson estimate: 73.06 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.97 % / Rmerge(I) obs: 0.512 / Num. unique all: 204 / Num. unique obs: 269 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA3

1ea3


Resolution: 3→21.926 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 42.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3213 119 5.47 %
Rwork0.2719 --
obs0.2751 2177 94.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→21.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 0 2 1131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031145
X-RAY DIFFRACTIONf_angle_d0.5951549
X-RAY DIFFRACTIONf_dihedral_angle_d13.517419
X-RAY DIFFRACTIONf_chiral_restr0.023189
X-RAY DIFFRACTIONf_plane_restr0.005193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0003-3.23130.4339200.3974407X-RAY DIFFRACTION94
3.2313-3.55520.4895240.373414X-RAY DIFFRACTION95
3.5552-4.06680.3895210.2918419X-RAY DIFFRACTION95
4.0668-5.1130.2526250.2506413X-RAY DIFFRACTION94
5.113-21.92630.2771290.2083405X-RAY DIFFRACTION94

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