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- PDB-6bk6: Crystal structure of Hendra virus matrix protein -

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Basic information

Entry
Database: PDB / ID: 6bk6
TitleCrystal structure of Hendra virus matrix protein
ComponentsHendra virus matrix protein
KeywordsVIRAL PROTEIN / Hendra virus / viral assembly
Function / homology
Function and homology information


virion component => GO:0044423 / virion assembly / virion component / host cell cytoplasm / structural constituent of virion / host cell nucleus
Similarity search - Function
Viral matrix protein / Viral matrix protein, C-terminal domain / Viral matrix protein, N-terminal domain / Viral matrix protein
Similarity search - Domain/homology
ACETATE ION / Matrix protein / Matrix protein
Similarity search - Component
Biological speciesHendra henipavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, Y.C.
CitationJournal: J. Virol. / Year: 2018
Title: Electrostatic Interactions between Hendra Virus Matrix Proteins Are Required for Efficient Virus-Like-Particle Assembly.
Authors: Liu, Y.C. / Grusovin, J. / Adams, T.E.
History
DepositionNov 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 27, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Oct 4, 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
Item: _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: Hendra virus matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3032
Polymers42,2441
Non-polymers591
Water1,11762
1
A: Hendra virus matrix protein
hetero molecules

A: Hendra virus matrix protein
hetero molecules


  • defined by author&software
  • Evidence: homology, The organisation of the dimeric Hendra matrix protein is similar to structurally characterised matrix proteins of paramyxoviruses, including RSV, NDV, and hMPV., gel filtration, ...Evidence: homology, The organisation of the dimeric Hendra matrix protein is similar to structurally characterised matrix proteins of paramyxoviruses, including RSV, NDV, and hMPV., gel filtration, Gel filtration chromatography analysis indicated higher oligomeric state of Hendra virus matrix protein.
  • 84.6 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)84,6064
Polymers84,4872
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area4870 Å2
ΔGint-18 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.380, 60.380, 364.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Hendra virus matrix protein


Mass: 42243.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra henipavirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F4YH69, UniProt: O89341*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ca-Acetate, 0.1 M imadazole pH 7.5, 5% PEG 8000

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953735 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953735 Å / Relative weight: 1
ReflectionResolution: 2.5→52.291 Å / Num. obs: 14447 / % possible obs: 98.8 % / Redundancy: 5.7 % / Net I/σ(I): 11.2
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1583 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GIO

4gio


Resolution: 2.5→52.291 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.51
RfactorNum. reflection% reflection
Rfree0.2466 708 4.9 %
Rwork0.2202 --
obs0.2216 14441 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→52.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 4 62 2317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142349
X-RAY DIFFRACTIONf_angle_d1.263161
X-RAY DIFFRACTIONf_dihedral_angle_d22.942889
X-RAY DIFFRACTIONf_chiral_restr0.086349
X-RAY DIFFRACTIONf_plane_restr0.007394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.69310.29931210.27312680X-RAY DIFFRACTION99
2.6931-2.9640.31161400.26172682X-RAY DIFFRACTION99
2.964-3.39290.28941350.23172742X-RAY DIFFRACTION99
3.3929-4.27440.23111350.19632733X-RAY DIFFRACTION97
4.2744-52.3020.21781770.20972896X-RAY DIFFRACTION96

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