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- PDB-4gh9: Crystal structure of Marburg virus VP35 RNA binding domain -

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Basic information

Entry
Database: PDB / ID: 4gh9
TitleCrystal structure of Marburg virus VP35 RNA binding domain
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / RNA BINDING PROTEIN / Viral polymerase / Interferon inhibition / double stranded viral RNA
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm
Similarity search - Function
Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses 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. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 ...Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses 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. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Polymerase cofactor VP35
Similarity search - Component
Biological speciesMarburg virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBale, S. / Jean-Philippe, J. / Bornholdt, Z.A. / Kimberlin, C.K. / Halfmann, P. / Zandonatti, M.A. / Kunert, J. / Kroon, G.J.A. / Kawaoka, Y. / MacRae, I.J. ...Bale, S. / Jean-Philippe, J. / Bornholdt, Z.A. / Kimberlin, C.K. / Halfmann, P. / Zandonatti, M.A. / Kunert, J. / Kroon, G.J.A. / Kawaoka, Y. / MacRae, I.J. / Wilson, I.A. / Saphire, E.O.
CitationJournal: Plos Pathog. / Year: 2012
Title: Marburg Virus VP35 Can Both Fully Coat the Backbone and Cap the Ends of dsRNA for Interferon Antagonism.
Authors: Bale, S. / Julien, J.P. / Bornholdt, Z.A. / Kimberlin, C.R. / Halfmann, P. / Zandonatti, M.A. / Kunert, J. / Kroon, G.J. / Kawaoka, Y. / Macrae, I.J. / Wilson, I.A. / Saphire, E.O.
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Sep 13, 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: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6577
Polymers16,3031
Non-polymers3546
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.524, 90.880, 65.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

21A-542-

HOH

31A-546-

HOH

41A-602-

HOH

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Components

#1: Protein Polymerase cofactor VP35


Mass: 16302.603 Da / Num. of mol.: 1 / Fragment: UNP residues 204-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marburg virus / Strain: Musoke / Gene: VP35 / Plasmid: pET46b / Production host: Escherichia coli (E. coli) / Strain (production host): R2 / References: UniProt: P35259
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.95 Å3/Da / Density % sol: 37.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2-2.4 M ammonium sulphate, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2010
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→45.44 Å / Num. obs: 15759 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 21.89 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 11.5
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1543 / Rsym value: 0.446 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS8

3ks8


Resolution: 1.65→26.682 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 1 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 783 4.98 %RANDOM
Rwork0.1608 ---
all0.1635 ---
obs0.1635 15720 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→26.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 24 117 1084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006983
X-RAY DIFFRACTIONf_angle_d1.0041330
X-RAY DIFFRACTIONf_dihedral_angle_d12.99356
X-RAY DIFFRACTIONf_chiral_restr0.067152
X-RAY DIFFRACTIONf_plane_restr0.005175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.75340.27451160.18572448X-RAY DIFFRACTION100
1.7534-1.88870.29691420.17562441X-RAY DIFFRACTION100
1.8887-2.07880.24341360.15842460X-RAY DIFFRACTION100
2.0788-2.37940.22511300.1422484X-RAY DIFFRACTION100
2.3794-2.99710.24231270.16052501X-RAY DIFFRACTION100
2.9971-26.6850.17841320.16342603X-RAY DIFFRACTION100

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