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- PDB-1ea3: Influenza virus M1 protein -

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Basic information

Entry
Database: PDB / ID: 1ea3
TitleInfluenza virus M1 protein
ComponentsMATRIX PROTEIN M1
KeywordsINFLUENZA VIRUS / MATRIX PROTEIN
Function / homology
Function and homology information


Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral mRNA Translation / viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / extracellular region / plasma 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsArzt, S.
CitationJournal: Virology / Year: 2001
Title: Combined Results from Solution Studies on Intact Influenza Virus M1 Protein and from a New Crystal Form of its N-Terminal Domain Show that M1 is an Elongated Monomeric
Authors: Arzt, S. / Baudin, F. / Barge, A. / Timmins, P. / Burmeister, W.P. / Ruigrok, R.W.
History
DepositionNov 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 24, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Source and taxonomy
Category: atom_site / entity_src_gen / pdbx_unobs_or_zero_occ_residues
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MATRIX PROTEIN M1
B: MATRIX PROTEIN M1


Theoretical massNumber of molelcules
Total (without water)36,4162
Polymers36,4162
Non-polymers00
Water1,45981
1
A: MATRIX PROTEIN M1


Theoretical massNumber of molelcules
Total (without water)18,2081
Polymers18,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MATRIX PROTEIN M1


Theoretical massNumber of molelcules
Total (without water)18,2081
Polymers18,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.860, 44.147, 47.692
Angle α, β, γ (deg.)77.10, 67.83, 77.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, -0.0065, -0.0009), (0.0064, 0.998, -0.0623), (0.0013, 0.0623, 0.9981)
Vector: 4.4392, -16.7038, 20.2821)

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Components

#1: Protein MATRIX PROTEIN M1


Mass: 18208.088 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN RESIDUES 1-164
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL DOMAIN RESIDUE 1-164 / Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/PR/8/34 / Plasmid: PET16B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P03485
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.99 Å3/Da / Density % sol: 37.84 %
Crystal growpH: 7
Details: 0.1M HEPES PH7.5, 5% V/V ISOPROPANOL,6-10% PEG4000, pH 7.00
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Details: drop contains protein and reservoir solution in a 1:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
210 mMTris-HCl1drop
3100 mM1dropNaCl
410 mMmercaptoethanol1drop
50.1 MHEPES1reservoir
65 %(v/v)isopropanol1reservoir
76-10 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 / Details: MULTILAYER
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→33.15 Å / Num. obs: 11585 / % possible obs: 97.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.1 Å2 / Rsym value: 0.067 / Net I/σ(I): 5.3
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.212 / % possible all: 97.1
Reflection
*PLUS
Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.212

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AA7

1aa7


Resolution: 2.3→14.98 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE OCCUPANCIES OF RESIDUES 72 - 75 IN CHAIN A AND 72 - 74 IN CHAIN B HAVE BEEN SET TO 0.0 BECAUSE OF THE LACK OF ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1121 9.9 %RANDOM
Rwork0.242 ---
obs0.242 11376 95.7 %-
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.27 Å21.49 Å2-3.08 Å2
2--5.67 Å2-1.94 Å2
3----0.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 0 81 2501
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
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: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 177 9.6 %
Rwork0.303 1667 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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