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- PDB-6oaf: Sudan virus nucleoprotein core domain in complex with VP35 chaper... -

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Basic information

Entry
Database: PDB / ID: 6oaf
TitleSudan virus nucleoprotein core domain in complex with VP35 chaperoning peptide
ComponentsPolymerase cofactor VP35,Nucleoprotein
KeywordsVIRAL PROTEIN / Complex SUDV NP-VP35
Function / homology
Function and homology information


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 / virion component => GO:0044423 / viral RNA genome packaging / helical viral capsid / 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 / ribonucleoprotein complex / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein / 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.
Similarity search - Domain/homology
Polymerase cofactor VP35 / Nucleoprotein
Similarity search - Component
Biological speciesSudan ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLanderas-Bueno, S. / Oda, S. / Norris, M.J. / Li Salie, Z. / Ollmann Saphire, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI118016 United States
CitationJournal: Mbio / Year: 2019
Title: Sudan Ebolavirus VP35-NP Crystal Structure Reveals a Potential Target for Pan-Filovirus Treatment.
Authors: Landeras-Bueno, S. / Oda, S.I. / Norris, M.J. / Li Salie, Z. / Guenaga, J. / Wyatt, R.T. / Saphire, E.O.
History
DepositionMar 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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,Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)42,7221
Polymers42,7221
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.840, 33.750, 101.860
Angle α, β, γ (deg.)90.00, 101.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Polymerase cofactor VP35,Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 42721.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus (strain Human/Uganda/Gulu/2000), (gene. exp.) Sudan ebolavirus (strain Boniface-76)
Strain: Human/Uganda/Gulu/2000, Boniface-76 / Gene: VP35, NP / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): R2 / References: UniProt: Q5XX07, UniProt: Q9QP77
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5
Details: 20% PEG3350, 0.2 M potassium fluoride pH 8.5, 0.1 M bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.2819 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2819 Å / Relative weight: 1
ReflectionResolution: 2.2→48.61 Å / Num. obs: 22033 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.049 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 1.361 / CC1/2: 0.49 / Rpim(I) all: 0.922

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZTG

4ztg


Resolution: 2.2→43.35 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 30.21
RfactorNum. reflection% reflection
Rfree0.2481 2091 5.05 %
Rwork0.2118 --
obs0.2136 22033 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 0 57 2857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032895
X-RAY DIFFRACTIONf_angle_d0.5643927
X-RAY DIFFRACTIONf_dihedral_angle_d13.1361051
X-RAY DIFFRACTIONf_chiral_restr0.025450
X-RAY DIFFRACTIONf_plane_restr0.002508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24790.41341270.40152276X-RAY DIFFRACTION83
2.2479-2.30410.38791280.34872427X-RAY DIFFRACTION94
2.3041-2.36640.32451400.33312579X-RAY DIFFRACTION98
2.3664-2.43610.31711480.32642736X-RAY DIFFRACTION99
2.4361-2.51470.3851360.31882582X-RAY DIFFRACTION99
2.5147-2.60460.27961440.28612699X-RAY DIFFRACTION99
2.6046-2.70880.32681390.26022614X-RAY DIFFRACTION99
2.7088-2.83210.30031420.24942692X-RAY DIFFRACTION100
2.8321-2.98140.30711380.24942675X-RAY DIFFRACTION100
2.9814-3.16810.3071430.24642627X-RAY DIFFRACTION100
3.1681-3.41260.28441450.22412713X-RAY DIFFRACTION100
3.4126-3.75590.20531390.19822659X-RAY DIFFRACTION100
3.7559-4.29890.2151440.16532664X-RAY DIFFRACTION100
4.2989-5.41460.17141410.15982660X-RAY DIFFRACTION100
5.4146-43.35850.23121370.17882674X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9466-1.3799-2.44581.57052.31266.03470.46170.54430.644-0.2477-0.0632-0.0915-0.67010.7904-0.32250.49770.05330.02080.79780.06650.47040.3214-13.08727.1579
24.32940.50321.4363.0052.63725.96910.1272-0.3464-0.04980.0647-0.31880.7656-0.0505-1.03970.1870.49270.04140.03470.55060.03040.6606-33.6934-14.626132.5209
36.44370.46074.42674.6621-5.15979.52060.1423-1.75-1.285-0.73530.23121.61390.7487-0.6724-0.42870.7962-0.14250.2131.05230.06311.2809-40.0602-23.605442.5632
43.16690.25070.52133.9712-0.03726.6840.142-0.28260.1250.25520.01050.1533-0.2301-0.388-0.16310.40960.03150.04430.3696-0.00450.4-18.8535-10.133738.3953
56.1934-1.0594-1.12832.5747-0.58483.59840.3150.7003-0.4281-0.1704-0.3027-0.53680.24170.92170.02660.44530.1233-0.0170.7198-0.10.55362.9021-22.650216.3872
63.57832.73450.1382.3950.14060.0068-0.03640.6556-0.5320.07650.163-0.01940.9751-0.0943-0.19490.81890.1646-0.18850.66190.00980.7186-22.9744-31.233117.4032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -13 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 240 )
5X-RAY DIFFRACTION5chain 'A' and (resid 241 through 356 )
6X-RAY DIFFRACTION6chain 'A' and (resid 15 through 42 )

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