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- PDB-5v6g: Crystal structure of Influenza A virus Matrix Protein M1(NLS-88R) -

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Basic information

Entry
Database: PDB / ID: 5v6g
TitleCrystal structure of Influenza A virus Matrix Protein M1(NLS-88R)
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / Influenza virus / Matrix protein / NLS-88R mutant / pH 5.5
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: 2 Å
AuthorsMusayev, F.N. / Safo, M.K. / Desai, U.R. / Xie, H. / Mosier, P.D. / Chiang, M.-J.
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 16, 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
D: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)76,3924
Polymers76,3924
Non-polymers00
Water14,790821
1
A: Matrix protein 1
B: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)38,1962
Polymers38,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-13 kcal/mol
Surface area13150 Å2
MethodPISA
2
C: Matrix protein 1
D: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)38,1962
Polymers38,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-11 kcal/mol
Surface area13090 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-37 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.746, 119.818, 59.684
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Matrix protein 1 / M1


Mass: 19098.055 Da / Num. of mol.: 4 / 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.: 821 / 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: 1.86 Å3/Da / Density % sol: 33.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein solution: 13.7 mg/ml in 55 mM K2HPO4/KH2PO4/H3PO4, 0.2M NaCl, 10 mM BME, pH 4.0 Reservoir solution: 75 mM Tris-HCl, pH 7.0, 15% PEG-1000

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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: Nov 24, 2012 / 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→29.95 Å / Num. obs: 33892 / % possible obs: 90 % / Redundancy: 6.05 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.97 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 3432 / % possible all: 91.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AA7

1aa7


Resolution: 2→29.84 Å / Rfactor Rfree error: 0.03 / Data cutoff high absF: 1818988.72 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1673 4.9 %RANDOM
Rwork0.192 ---
obs0.192 33843 89.8 %-
Solvent computationBsol: 47.3369 Å2 / ksol: 0.236175 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å21.56 Å2
2---3.66 Å20 Å2
3---3.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.22 Å
Refinement stepCycle: 1 / Resolution: 2→29.84 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.305 170 5 %
Rwork0.24 3258 -
obs--91.8 %

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