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- PDB-7k5l: Ebola virus VP40 octameric ring generated by an RNA oligonucleotide -

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Basic information

Entry
Database: PDB / ID: 7k5l
TitleEbola virus VP40 octameric ring generated by an RNA oligonucleotide
Components
  • HSP RNA oligonucleotide
  • Matrix protein VP40
KeywordsVIRAL PROTEIN / Ebola virus / transformer protein / RNA 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
RNA / RNA (> 10) / Matrix protein VP40
Similarity search - Component
Biological speciesZaire ebolavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 17, 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 RNA oligonucleotide


Theoretical massNumber of molelcules
Total (without water)30,1742
Polymers30,1742
Non-polymers00
Water1,78399
1
A: Matrix protein VP40
R: HSP RNA oligonucleotide
x 8


Theoretical massNumber of molelcules
Total (without water)241,39516
Polymers241,39516
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
Buried area28930 Å2
ΔGint-173 kcal/mol
Surface area40300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.626, 80.626, 47.083
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-351-

HOH

21A-396-

HOH

31R-102-

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: RNA chain HSP RNA oligonucleotide


Mass: 11056.526 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.: 99 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 1 uL 3.5 mg/mL protein, 1 uL 75 mM sodium citrate tribasic pH 8.4, 150 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2019
RadiationMonochromator: CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.38→80.63 Å / Num. obs: 30977 / % possible obs: 95.7 % / Redundancy: 24.8 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.8
Reflection shellResolution: 1.38→1.41 Å / Redundancy: 25.7 % / Rmerge(I) obs: 1.519 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1580 / CC1/2: 0.853 / % possible all: 100

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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: 1.38→23.54 Å / SU ML: 0.1347 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3609
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 1555 5.03 %
Rwork0.1802 29389 -
obs0.181 30944 95.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.21 Å2
Refinement stepCycle: LAST / Resolution: 1.38→23.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 65 0 99 1114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481090
X-RAY DIFFRACTIONf_angle_d0.78411515
X-RAY DIFFRACTIONf_chiral_restr0.0716182
X-RAY DIFFRACTIONf_plane_restr0.0058182
X-RAY DIFFRACTIONf_dihedral_angle_d8.8708177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.430.29821550.28592739X-RAY DIFFRACTION100
1.43-1.480.28141420.26372755X-RAY DIFFRACTION99.97
1.48-1.540.26021490.22582723X-RAY DIFFRACTION99.93
1.54-1.610.20881610.19712731X-RAY DIFFRACTION99.79
1.61-1.690.25171300.19162774X-RAY DIFFRACTION99.9
1.69-1.80.22061600.18552749X-RAY DIFFRACTION99.93
1.8-1.940.22561120.18532393X-RAY DIFFRACTION86.08
1.94-2.130.21871310.17972358X-RAY DIFFRACTION84.57
2.13-2.440.18231470.17692808X-RAY DIFFRACTION99.97
2.44-3.070.20431240.18142510X-RAY DIFFRACTION87.95
3.07-23.540.16291440.16332849X-RAY DIFFRACTION94.3

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