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- PDB-5v7s: Crystal structure of Influenza A virus matrix protein M1 (NLS-88E... -

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Basic information

Entry
Database: PDB / ID: 5v7s
TitleCrystal structure of Influenza A virus matrix protein M1 (NLS-88E, pH 6.2)
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / Influenza A / Matrix protein / NLS-88E mutant / pH 6.2
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
PHOSPHATE ION / Matrix protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMusayev, F.N. / Safo, M.K. / Althufairi, B. / Desai, U.R. / Xie, H. / Mosier, P.D. / Chiang, M.-J. / Zhou, Q.
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 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 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

Downloads & links

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Assembly

Deposited unit
A: Matrix protein 1
B: Matrix protein 1
C: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4005
Polymers57,2103
Non-polymers1902
Water23413
1
B: Matrix protein 1
C: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2353
Polymers38,1402
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Matrix protein 1
hetero molecules

A: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3304
Polymers38,1402
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3040 Å2
ΔGint-26 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.612, 133.260, 39.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Matrix protein 1 / M1


Mass: 19069.975 Da / Num. of mol.: 3 / Mutation: G88E, 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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Protein solution: 8 mg/ml in 50mM K2HPO4/KH2PO4/H3PO4, 0.2M NaCl, 10mM bME, pH 3.2 Reservoir solution: 0.1M Tris-HCl, pH 8.2, 8% PEG-8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 20, 2015 / Details: Rigaku varimax confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→26.23 Å / Num. obs: 14742 / % possible obs: 90.7 % / Redundancy: 5.37 % / Biso Wilson estimate: 55.06 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.51 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1473 / % possible all: 91.9

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Processing

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

1ea3


Resolution: 2.5→26.23 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.93
RfactorNum. reflection% reflectionSelection details
Rfree0.3115 767 5.21 %RANDOM
Rwork0.2203 ---
obs0.2251 14714 90.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→26.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 10 14 3659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093705
X-RAY DIFFRACTIONf_angle_d1.1655009
X-RAY DIFFRACTIONf_dihedral_angle_d17.9181373
X-RAY DIFFRACTIONf_chiral_restr0.042593
X-RAY DIFFRACTIONf_plane_restr0.006633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.69290.4171540.30212764X-RAY DIFFRACTION92
2.6929-2.96350.34951530.29472774X-RAY DIFFRACTION92
2.9635-3.39160.41911540.28422749X-RAY DIFFRACTION90
3.3916-4.270.31421390.21282728X-RAY DIFFRACTION88

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