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- PDB-7k5d: Ebola virus VP40 octameric ring generated by a DNA oligonucleotide -

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Basic information

Entry
Database: PDB / ID: 7k5d
TitleEbola virus VP40 octameric ring generated by a DNA oligonucleotide
Components
  • HSP DNA oligonucleotide
  • Matrix protein VP40
KeywordsVIRAL PROTEIN / Ebola virus / transformer protein / DNA binding protein / matrix protein
Function / homology
Function and homology information


intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / symbiont-mediated perturbation of host cell cycle progression / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane ...intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / symbiont-mediated perturbation of host cell cycle progression / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane / host cell / structural constituent of virion / membrane raft / ribonucleoprotein complex / host cell plasma membrane / virion membrane / RNA binding / extracellular region / identical protein binding
Similarity search - Function
EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40
Similarity search - Domain/homology
DNA / DNA (> 10) / Matrix protein VP40
Similarity search - Component
Biological speciesZaire ebolavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLanderas-Bueno, S. / Wasserman, H. / Salie, Z.L. / Saphire, E.O.
CitationJournal: Cell Rep / Year: 2021
Title: Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form.
Authors: Landeras-Bueno, S. / Wasserman, H. / Oliveira, G. / VanAernum, Z.L. / Busch, F. / Salie, Z.L. / Wysocki, V.H. / Andersen, K. / Saphire, E.O.
History
DepositionSep 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Matrix protein VP40
R: HSP DNA oligonucleotide


Theoretical massNumber of molelcules
Total (without water)29,7832
Polymers29,7832
Non-polymers00
Water1,54986
1
A: Matrix protein VP40
R: HSP DNA oligonucleotide

A: Matrix protein VP40
R: HSP DNA oligonucleotide

A: Matrix protein VP40
R: HSP DNA oligonucleotide

A: Matrix protein VP40
R: HSP DNA oligonucleotide

A: Matrix protein VP40
R: HSP DNA oligonucleotide

A: Matrix protein VP40
R: HSP DNA oligonucleotide

A: Matrix protein VP40
R: HSP DNA oligonucleotide

A: Matrix protein VP40
R: HSP DNA oligonucleotide


Theoretical massNumber of molelcules
Total (without water)238,26116
Polymers238,26116
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)80.438, 80.438, 47.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422
Space group name HallP42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

21R-101-

HOH

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Components

#1: Protein Matrix protein VP40 / Ebola VP40 / eVP40 / Membrane-associated protein VP40


Mass: 19117.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: VP40 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05128
#2: DNA chain HSP DNA oligonucleotide


Mass: 10664.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.28 Å3/Da / Density % sol: 4.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 1 uL 3.5 mg/mL protein, 1 uL 75 mM sodium citrate tribasic pH 6.6, 150 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100.5 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2019
RadiationMonochromator: CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.78→40.76 Å / Num. obs: 15385 / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 27.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.5
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 844 / CC1/2: 0.874 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LDM

4ldm


Resolution: 1.78→40.76 Å / SU ML: 0.1979 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3601
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 757 4.92 %
Rwork0.1819 14620 -
obs0.1827 15377 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.5 Å2
Refinement stepCycle: LAST / Resolution: 1.78→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 62 0 86 1090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711075
X-RAY DIFFRACTIONf_angle_d0.92861490
X-RAY DIFFRACTIONf_chiral_restr0.0572177
X-RAY DIFFRACTIONf_plane_restr0.0064177
X-RAY DIFFRACTIONf_dihedral_angle_d12.9439170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.920.25331410.2222848X-RAY DIFFRACTION99.57
1.92-2.110.20091530.18472862X-RAY DIFFRACTION100
2.11-2.420.19321480.18092892X-RAY DIFFRACTION99.9
2.42-3.050.2231640.19162908X-RAY DIFFRACTION99.93
3.05-40.760.18161510.17363110X-RAY DIFFRACTION99.79

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