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- PDB-5t3w: Marburg virus VP30 bound to nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 5t3w
TitleMarburg virus VP30 bound to nucleoprotein
ComponentsFusion protein of Nucleoprotein and Minor nucleoprotein VP30
KeywordsVIRAL PROTEIN / transcription / replication / co-factor / regulator
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / metal ion 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 speciesLake Victoria marburgvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsKirchdoerfer, R.K. / 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 / diffrn_radiation_wavelength / 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


Theoretical massNumber of molelcules
Total (without water)161,3578
Polymers161,3578
Non-polymers00
Water0
1
A: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
B: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30


Theoretical massNumber of molelcules
Total (without water)40,3392
Polymers40,3392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-50 kcal/mol
Surface area13180 Å2
MethodPISA
2
C: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
D: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30


Theoretical massNumber of molelcules
Total (without water)40,3392
Polymers40,3392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-52 kcal/mol
Surface area13110 Å2
MethodPISA
3
E: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
F: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30


Theoretical massNumber of molelcules
Total (without water)40,3392
Polymers40,3392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-51 kcal/mol
Surface area13080 Å2
MethodPISA
4
G: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30
H: Fusion protein of Nucleoprotein and Minor nucleoprotein VP30


Theoretical massNumber of molelcules
Total (without water)40,3392
Polymers40,3392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-48 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.143, 106.143, 375.573
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 20169.670 Da / Num. of mol.: 8
Fragment: UNP P27588 residues 552-579,UNP P35258 residues 146-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Musoke-80)
Strain: Musoke-80 / Gene: NP, VP30 / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: P27588, UniProt: P35258

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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: 3.79 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% isopropanol, 18% PEG 4000, 0.1M sodium citrate pH 5.6 using 0.2 uL 24.7 mg/mL protein mixed with 0.2 uL mother liquor

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.7502 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7502 Å / Relative weight: 1
ReflectionResolution: 3.25→125.191 Å / Num. obs: 39861 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 126.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.9
Reflection shellResolution: 3.25→3.38 Å / Redundancy: 19.5 % / Rmerge(I) obs: 2.96 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.61 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSOct 15, 2015data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DVW

5dvw


Resolution: 3.25→125.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 1.127 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24082 1939 4.9 %RANDOM
Rwork0.21261 ---
obs0.21401 37850 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 143.111 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20.71 Å20 Å2
2--1.43 Å2-0 Å2
3----4.63 Å2
Refinement stepCycle: LAST / Resolution: 3.25→125.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8624 0 0 0 8624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198800
X-RAY DIFFRACTIONr_bond_other_d00.028416
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.95811952
X-RAY DIFFRACTIONr_angle_other_deg3.351319344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.89651080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.80824.8400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.616151504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1491540
X-RAY DIFFRACTIONr_chiral_restr0.0470.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219912
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022000
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_it10.20814.324368
X-RAY DIFFRACTIONr_mcbond_other10.20814.3194367
X-RAY DIFFRACTIONr_mcangle_it13.76621.4665432
X-RAY DIFFRACTIONr_mcangle_other13.76521.4675433
X-RAY DIFFRACTIONr_scbond_it15.22314.5624432
X-RAY DIFFRACTIONr_scbond_other15.22114.5624433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.96521.7086521
X-RAY DIFFRACTIONr_long_range_B_refined17.55410246
X-RAY DIFFRACTIONr_long_range_B_other17.55410247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 159 -
Rwork0.409 2740 -
obs--100 %

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