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- PDB-4hi6: Crystal structure of H112W mutant of borna disease virus matrix p... -

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Basic information

Entry
Database: PDB / ID: 4hi6
TitleCrystal structure of H112W mutant of borna disease virus matrix protein
ComponentsMatrix protein
KeywordsVIRAL PROTEIN / VIRAL MATRIX PROTEIN / RNA BINDING / MEMBRANE BINDING / VIRUSES / SSRNA NEGATIVE-STRAND VIRUSES / MONONEGAVIRALES / BORNAVIRIDAE / BORNAVIRUS / VIRION
Function / homology
Function and homology information


virion component / structural constituent of virion / host cell cytoplasm / host cell plasma membrane / identical protein binding / membrane
Similarity search - Function
Borna disease virus, matrix protein / Matrix protein, Bornaviridae / Matrix protein superfamily / ssRNA-binding matrix protein of Bornaviridae / Topoisomerase I; domain 3 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
GUANOSINE-3'-MONOPHOSPHATE / Matrix protein
Similarity search - Component
Biological speciesBorna disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDautel, P. / Kolenko, P. / Stubbs, M.T.
CitationJournal: To be Published
Title: Matrix protein variants provide support for alternative Borna disease virus infection pathway
Authors: Dautel, P. / Kolenko, P. / Stubbs, M.T.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,20711
Polymers65,3044
Non-polymers9047
Water1,71195
1
A: Matrix protein
B: Matrix protein
C: Matrix protein
D: Matrix protein
hetero molecules

A: Matrix protein
B: Matrix protein
C: Matrix protein
D: Matrix protein
hetero molecules

A: Matrix protein
B: Matrix protein
C: Matrix protein
D: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,62233
Polymers195,91112
Non-polymers2,71121
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area42480 Å2
ΔGint-281 kcal/mol
Surface area63050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.066, 158.066, 103.714
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Matrix protein / gp18 / p16


Mass: 16325.882 Da / Num. of mol.: 4 / Mutation: H112W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus / Gene: M / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0C794
#2: Chemical ChemComp-3GP / GUANOSINE-3'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.82 Å3/Da / Density % sol: 67.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MgCl2, 12% (w/v) PEG6000, 0.1 M N-(2-Acetamido)iminodiacetic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.151
11K, H, -L20.849
ReflectionResolution: 2.2→50 Å / Num. obs: 49036 / % possible obs: 99.8 % / Observed criterion σ(I): -3.7 / Redundancy: 2.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.1 / % possible all: 96

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F1J

3f1j


Resolution: 2.2→48.49 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0 / SU B: 1.896 / SU ML: 0.054 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rwork0.219 ---
obs0.223 49036 100 %-
all-49036 --
Rfree---RANDOM
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.45 Å2
Baniso -1Baniso -2Baniso -3
1--14.27 Å2-0 Å2-0 Å2
2---14.27 Å2-0 Å2
3---28.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4413 0 53 95 4561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194581
X-RAY DIFFRACTIONr_bond_other_d0.0010.024451
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9916225
X-RAY DIFFRACTIONr_angle_other_deg0.764310243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5423.659205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83615791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7191527
X-RAY DIFFRACTIONr_chiral_restr0.2010.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021066
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.246 3598

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