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- PDB-5toi: Crystal Structure of the Marburg Virus VP35 Oligomerization Domai... -

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Basic information

Entry
Database: PDB / ID: 5toi
TitleCrystal Structure of the Marburg Virus VP35 Oligomerization Domain P4222
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / polymerase cofactor / coiled coil / oligomerization / trimer
Function / homologyFiloviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / viral nucleocapsid / host cell cytoplasm / Polymerase cofactor VP35
Function and homology information
Biological speciesLake Victoria marburgvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsBruhn, J.F. / Tickle, I.J. / Bricogne, G. / Saphire, E.O.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007606 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI118016 United States
Burroughs Wellcome Fund United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
CitationJournal: J. Virol. / Year: 2017
Title: Crystal Structure of the Marburg Virus VP35 Oligomerization Domain.
Authors: Bruhn, J.F. / Kirchdoerfer, R.N. / Urata, S.M. / Li, S. / Tickle, I.J. / Bricogne, G. / Saphire, E.O.
History
DepositionOct 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Feb 8, 2017Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 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

Downloads & links

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Assembly

Deposited unit
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)24,6173
Polymers24,6173
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-54 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.490, 46.490, 310.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein Polymerase cofactor VP35


Mass: 8205.597 Da / Num. of mol.: 3 / Fragment: UNP residues 60-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Musoke-80)
Strain: Musoke-80 / Gene: VP35 / Production host: Escherichia coli (E. coli) / References: UniProt: P35259
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop
Details: 0.2 M K/Na tartrate and 40% 2-methyl-2,4-pentanediol (MPD)
PH range: 8.4 - 9.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.19→46.49 Å / Num. obs: 6946 / % possible obs: 34.7 % / Redundancy: 11 % / Biso Wilson estimate: 46.9 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.492 / Net I/σ(I): 12.1
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 3 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.418 / % possible all: 1

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.2data extraction
Aimlessdata scaling
XDSdata reduction
PHASERphasing
STARANISOdata scaling
BUSTER2.11.7refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TOH

5toh


Resolution: 2.19→42.42 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.869 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.518
RfactorNum. reflection% reflectionSelection details
Rfree0.342 704 10.14 %RANDOM
Rwork0.312 ---
obs0.315 6945 36.9 %-
Displacement parametersBiso max: 151.43 Å2 / Biso mean: 66.19 Å2 / Biso min: 3.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.5153 Å20 Å20 Å2
2--1.5153 Å20 Å2
3----3.0305 Å2
Refine analyzeLuzzati coordinate error obs: 0.68 Å
Refinement stepCycle: final / Resolution: 2.19→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 0 14 1676
Biso mean---18.15 -
Num. residues----208
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d807SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes482HARMONIC5
X-RAY DIFFRACTIONt_it3430HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion248SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3449SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3430HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg6258HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion4.99
X-RAY DIFFRACTIONt_other_torsion16.36
LS refinement shellResolution: 2.19→2.45 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.355 23 11.5 %
Rwork0.325 177 -
all-200 -
obs--3.85 %

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