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- PDB-4hiw: Crystal structure of R34/53A, H112W mutant of borna disease virus... -

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Basic information

Entry
Database: PDB / ID: 4hiw
TitleCrystal structure of R34/53A, 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 / BORNA VIRUS / VIRION
Function / homology
Function and homology information


virion component / host cell cytoplasm / structural constituent of virion / 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
Biological speciesBorna disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: 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

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Assembly

Deposited unit
A: Matrix protein


Theoretical massNumber of molelcules
Total (without water)16,1541
Polymers16,1541
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Matrix protein

A: Matrix protein

A: Matrix protein

A: Matrix protein


Theoretical massNumber of molelcules
Total (without water)64,6154
Polymers64,6154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation20_555x,-z,y1
Buried area8450 Å2
ΔGint-40 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.804, 136.804, 136.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Matrix protein / gp18 / p16


Mass: 16153.649 Da / Num. of mol.: 1 / Mutation: R34A, R53A, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0 M NaCl, 0.1 M NaH2PO4, 0.1 M KH2PO4, 0.1 M MES, 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 Å
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
ReflectionResolution: 2.9→50 Å / Num. all: 5121 / Num. obs: 5121 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 8.9 % / Biso Wilson estimate: 91 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 13.6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2.8 / Num. unique all: 722 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F1J

3f1j


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.94 / SU B: 11.447 / SU ML: 0.213 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.762 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE RFREE FLAGS WERE USED FOR REFINEMENT IN THE LAST CYCLE
RfactorNum. reflection% reflectionSelection details
Rwork0.1947 ---
all0.2042 5121 --
obs0.2042 5108 99.65 %-
Rfree-235 -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: 55.833 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 0 9 1109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021128
X-RAY DIFFRACTIONr_bond_other_d0.0060.02779
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9791529
X-RAY DIFFRACTIONr_angle_other_deg0.93631904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3935134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37724.08249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76815197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.223155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02230
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.341 320

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