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- PDB-4pus: Crystal Structure of Influenza A Virus Matrix Protein M1 -

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Basic information

Entry
Database: PDB / ID: 4pus
TitleCrystal Structure of Influenza A Virus Matrix Protein M1
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / flu / H1N1 / oligomerization / four-helix bundle / virion assembly / infection
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: 2.2 Å
AuthorsSafo, M.K. / Musayev, F.N. / Mosier, P.D. / Xie, H. / Desai, U.R.
CitationJournal: Plos One / Year: 2014
Title: Crystal structures of influenza a virus matrix protein m1: variations on a theme.
Authors: Safo, M.K. / Musayev, F.N. / Mosier, P.D. / Zhou, Q. / Xie, H. / Desai, U.R.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)38,2762
Polymers38,2762
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-8 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.300, 37.346, 94.974
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Matrix protein 1 / Matrix protein M1


Mass: 19138.145 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 2-165)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Wilson-Smith/1933 H1N1 / Gene: M / Plasmid: pET30b / 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.: 158 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: protein in 55 mM phosphate, 0.2 M sodium chloride, 2 mM TCEP, pH 4.0, precipitant: 15% PEG3000, 75 mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Feb 22, 2013
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→27.99 Å / Num. all: 19284 / Num. obs: 19111 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1841

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1EA3 AND 1AA7

1ea3

1aa7


Resolution: 2.2→27.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1085064.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 972 5.1 %RANDOM
Rwork0.226 ---
obs0.226 18971 98.3 %-
all-18971 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.094 Å2 / ksol: 0.306904 e/Å3
Displacement parametersBiso mean: 56.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.63 Å20 Å24.27 Å2
2--3.36 Å20 Å2
3----5.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 0 158 2394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.316 102 5.6 %
Rwork0.283 1729 -
obs--98.5 %

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