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- PDB-4ibb: Ebola virus VP35 bound to small molecule -

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Basic information

Entry
Database: PDB / ID: 4ibb
TitleEbola virus VP35 bound to small molecule
ComponentsPolymerase cofactor VP35
KeywordsTRANSCRIPTION/TRANSCRIPTION inhibitor / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Interferon inhibitory domain / TRANSCRIPTION-TRANSCRIPTION inhibitor complex
Function / homology
Function and homology information


suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / : / positive regulation of protein sumoylation ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / : / positive regulation of protein sumoylation / molecular sequestering activity / viral transcription / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / negative regulation of gene expression / RNA binding
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
Chem-1DK / Polymerase cofactor VP35
Similarity search - Component
Biological speciesEbola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsBrown, C.S. / Leung, D.W. / Xu, W. / Borek, D.M. / Otwinowski, Z. / Ramanan, P. / Stubbs, A.J. / Peterson, D.S. / Binning, J.M. / Amarasinghe, G.K. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Mol.Biol. / Year: 2014
Title: In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity.
Authors: Brown, C.S. / Lee, M.S. / Leung, D.W. / Wang, T. / Xu, W. / Luthra, P. / Anantpadma, M. / Shabman, R.S. / Melito, L.M. / Macmillan, K.S. / Borek, D.M. / Otwinowski, Z. / Ramanan, P. / ...Authors: Brown, C.S. / Lee, M.S. / Leung, D.W. / Wang, T. / Xu, W. / Luthra, P. / Anantpadma, M. / Shabman, R.S. / Melito, L.M. / Macmillan, K.S. / Borek, D.M. / Otwinowski, Z. / Ramanan, P. / Stubbs, A.J. / Peterson, D.S. / Binning, J.M. / Tonelli, M. / Olson, M.A. / Davey, R.A. / Ready, J.M. / Basler, C.F. / Amarasinghe, G.K.
History
DepositionDec 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Structure summary
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Structure summary / Category: audit_author / software
Item: _audit_author.name / _software.classification ..._audit_author.name / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3444
Polymers28,4212
Non-polymers9232
Water2,576143
1
A: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6722
Polymers14,2111
Non-polymers4621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6722
Polymers14,2111
Non-polymers4621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.480, 65.810, 72.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polymerase cofactor VP35


Mass: 14210.523 Da / Num. of mol.: 2 / Fragment: unp residues 215-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Strain: Mayinga-76 / Gene: VP35 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05127
#2: Chemical ChemComp-1DK / {4-[(5R)-3-hydroxy-2-oxo-4-(thiophen-2-ylcarbonyl)-5-(2,4,5-trimethylphenyl)-2,5-dihydro-1H-pyrrol-1-yl]phenyl}acetic acid


Mass: 461.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H23NO5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM magnesium acetate, pH7.5, 15% PEG3350, 10% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9785724 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785724 Å / Relative weight: 1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.752→36.111 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.19 / σ(F): 1.37 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 2141 10.11 %
Rwork0.1794 --
obs0.1841 19048 83.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.0601 Å2
Refinement stepCycle: LAST / Resolution: 1.752→36.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 66 143 2126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072100
X-RAY DIFFRACTIONf_angle_d1.2242870
X-RAY DIFFRACTIONf_dihedral_angle_d16.352834
X-RAY DIFFRACTIONf_chiral_restr0.038309
X-RAY DIFFRACTIONf_plane_restr0.005379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7523-1.79310.3426850.2168827X-RAY DIFFRACTION55
1.7931-1.83790.2531990.2148912X-RAY DIFFRACTION61
1.8379-1.88760.35681380.1949951X-RAY DIFFRACTION66
1.8876-1.94320.24761270.19021033X-RAY DIFFRACTION70
1.9432-2.00590.23741420.18711155X-RAY DIFFRACTION78
2.0059-2.07760.23271310.1861271X-RAY DIFFRACTION85
2.0776-2.16070.21581370.19031336X-RAY DIFFRACTION89
2.1607-2.25910.25651640.19461362X-RAY DIFFRACTION91
2.2591-2.37810.24191500.19221357X-RAY DIFFRACTION91
2.3781-2.52710.23061300.18531380X-RAY DIFFRACTION90
2.5271-2.72220.21551400.20131368X-RAY DIFFRACTION90
2.7222-2.9960.25521690.19691403X-RAY DIFFRACTION92
2.996-3.42920.22031640.18951516X-RAY DIFFRACTION98
3.4292-4.31930.21021720.15941545X-RAY DIFFRACTION100
4.3193-36.11920.19971930.15631617X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.097 Å / Origin y: 29.2881 Å / Origin z: 11.713 Å
111213212223313233
T0.1469 Å2-0.0141 Å2-0.0053 Å2-0.0844 Å2-0.0051 Å2--0.2077 Å2
L0.3251 °2-0.0242 °2-0.8093 °2--0.0014 °20.0584 °2--2.0245 °2
S-0.0061 Å °0.0022 Å °-0.0038 Å °-0.0173 Å °0.016 Å °-0.0089 Å °0.0375 Å °-0.1342 Å °-0.0031 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA218 - 340
2X-RAY DIFFRACTION1allB217 - 340
3X-RAY DIFFRACTION1allB1 - 401
4X-RAY DIFFRACTION1allA1 - 401
5X-RAY DIFFRACTION1allB1 - 561
6X-RAY DIFFRACTION1allA1 - 402

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