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- PDB-3f1j: Crystal structure of the Borna disease virus matrix protein (BDV-... -

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Basic information

Entry
Database: PDB / ID: 3f1j
TitleCrystal structure of the Borna disease virus matrix protein (BDV-M) reveals RNA binding properties
ComponentsMatrix protein
KeywordsVIRAL PROTEIN / Viral matrix protein / RNA binding / membrane binding / Viruses / ssRNA negative-strand viruses / Mononegavirales / Bornaviridae / Bornavirus / Alternative splicing / Cytoplasm / Virion
Function / homology
Function and homology information


virion component => GO:0044423 / 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
CYTIDINE-5'-MONOPHOSPHATE / Matrix protein / Matrix protein
Similarity search - Component
Biological speciesBorna disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsNeumann, P. / Lieber, D. / Meyer, S. / Dautel, P. / Kerth, A. / Kraus, I. / Garten, W. / Stubbs, M.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of the Borna disease virus matrix protein (BDV-M) reveals ssRNA binding properties
Authors: Neumann, P. / Lieber, D. / Meyer, S. / Dautel, P. / Kerth, A. / Kraus, I. / Garten, W. / Stubbs, M.T.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9835
Polymers16,3721
Non-polymers6114
Water70339
1
A: Matrix protein
hetero molecules

A: Matrix protein
hetero molecules

A: Matrix protein
hetero molecules

A: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,93220
Polymers65,4864
Non-polymers2,44616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation23_555-z,y,x1
Buried area12500 Å2
ΔGint-142 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.570, 143.570, 143.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-303-

SO4

31A-228-

HOH

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Components

#1: Protein Matrix protein / gp18 / p16


Mass: 16371.610 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus / Gene: M / Plasmid: pMAL-c2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P52637, UniProt: P0C794*PLUS
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 8000, 0.5M Li2SO4, 0.1M Tris/HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9500, 0.97920, 0.97950
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 20, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97921
30.97951
ReflectionNumber: 59411 / Rmerge(I) obs: 0.091 / D res high: 2.59 Å / Num. obs: 14675 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
102021188.310.066
61092198.210.069
5687999.410.068
45196799.610.071
34552999.910.109
2.83218899.610.315
2.72.8135899.310.469
2.592.7162294.410.628
ReflectionResolution: 2.65→20 Å / Num. all: 7660 / Num. obs: 7570 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.46 % / Biso Wilson estimate: 67.809 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.099 / Net I/σ(I): 11.97
Reflection shellResolution: 2.65→2.8 Å / Redundancy: 7.68 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 3.1 / Num. measured obs: 8630 / Num. unique all: 1133 / Num. unique obs: 1123 / Rsym value: 0.671 / % possible all: 99.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
DMphasing
CNS1.1refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→19.54 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.836 / Data cutoff high absF: 11301727 / 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
Rfree0.264 570 7.6 %RANDOM
Rwork0.217 ---
all0.221 7660 --
obs0.221 7491 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.411 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso max: 106.19 Å2 / Biso mean: 61.819 Å2 / Biso min: 35.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-8 Å
Luzzati sigma a0.31 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 36 39 1257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.671.5
X-RAY DIFFRACTIONc_mcangle_it2.972
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2.65→2.77 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.278 67 7.5 %
Rwork0.275 831 -
all-898 -
obs-898 95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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