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- PDB-5t3t: Ebola virus VP30 CTD bound to nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 5t3t
TitleEbola virus VP30 CTD bound to nucleoprotein
ComponentsFusion protein of Nucleoprotein and Minor nucleoprotein VP30
KeywordsVIRAL PROTEIN / transcription / replication / regulator / co-factor
Function / homology
Function and homology information


symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / positive regulation of viral transcription / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / single-stranded RNA binding / ribonucleoprotein complex / virus-mediated perturbation of host defense response ...symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / positive regulation of viral transcription / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / single-stranded RNA binding / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding / zinc ion binding / identical protein binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1160 / Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30 / Ebola nucleoprotein / Ebola nucleoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoprotein / Transcriptional activator VP30
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKirchdoerfer, R.N. / Moyer, C.L. / Abelson, D.M. / Saphire, E.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI118016 United States
CitationJournal: Plos Pathog. / Year: 2016
Title: The Ebola Virus VP30-NP Interaction Is a Regulator of Viral RNA Synthesis.
Authors: Kirchdoerfer, R.N. / Moyer, C.L. / Abelson, D.M. / Saphire, E.O.
History
DepositionAug 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
B: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
C: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
D: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
E: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
F: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
G: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
H: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
I: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
J: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,88937
Polymers218,29610
Non-polymers2,59427
Water15,403855
1
A: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
B: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0436
Polymers43,6592
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-41 kcal/mol
Surface area13220 Å2
MethodPISA
2
C: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
D: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0436
Polymers43,6592
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-39 kcal/mol
Surface area12760 Å2
MethodPISA
3
E: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
F: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3329
Polymers43,6592
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-43 kcal/mol
Surface area12910 Å2
MethodPISA
4
G: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
H: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2368
Polymers43,6592
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-41 kcal/mol
Surface area13030 Å2
MethodPISA
5
I: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
J: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2368
Polymers43,6592
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-39 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.875, 116.784, 95.038
Angle α, β, γ (deg.)90.00, 108.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fusion protein of Nucleoprotein and Minor nucleoprotein VP30 / Nucleocapsid protein / Protein N / Transcription activator VP30


Mass: 21829.564 Da / Num. of mol.: 10
Fragment: UNP P18272 residues 600-627,UNP Q05323 residues 139-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: NP, VP30 / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: P18272, UniProt: Q05323
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 0.3 uL of 20 mg/mL protein mixed with 0.3 uL of 2.2 M ammonium sulfate, 100 mM sodium acetate pH 4.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2→90.12 Å / Num. obs: 89012 / % possible obs: 98.6 % / Redundancy: 3 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.57 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSJanuary 10, 2014data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I8B

2i8b


Resolution: 2.2→90.12 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24925 4477 5 %RANDOM
Rwork0.21416 ---
obs0.21593 84507 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.261 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.62 Å2
2---3.41 Å20 Å2
3---3.28 Å2
Refinement stepCycle: 1 / Resolution: 2.2→90.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10805 0 135 855 11795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911105
X-RAY DIFFRACTIONr_bond_other_d00.0210999
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.98215063
X-RAY DIFFRACTIONr_angle_other_deg3.884325219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.70751343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66322.898452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.818152002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.63715100
X-RAY DIFFRACTIONr_chiral_restr0.0990.21810
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112005
X-RAY DIFFRACTIONr_gen_planes_other0.010.022473
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3374.1325432
X-RAY DIFFRACTIONr_mcbond_other3.3264.1325431
X-RAY DIFFRACTIONr_mcangle_it3.9836.1666755
X-RAY DIFFRACTIONr_mcangle_other3.9896.1666756
X-RAY DIFFRACTIONr_scbond_it5.3324.525673
X-RAY DIFFRACTIONr_scbond_other5.2324.4915566
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5026.548147
X-RAY DIFFRACTIONr_long_range_B_refined7.01748.29512032
X-RAY DIFFRACTIONr_long_range_B_other7.01247.89311848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 286 -
Rwork0.334 6040 -
obs--94.9 %

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