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- PDB-4m0q: Ebola virus VP24 structure -

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Basic information

Entry
Database: PDB / ID: 4m0q
TitleEbola virus VP24 structure
ComponentsMembrane-associated protein VP24
KeywordsVIRAL PROTEIN / Ebola virus virulence factor
Function / homology
Function and homology information


host cell endomembrane system / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral budding from plasma membrane / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Filovirus membrane-associated VP24 / Filovirus membrane-associated protein VP24
Similarity search - Domain/homology
Membrane-associated protein VP24
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.921 Å
AuthorsXu, W. / Leung, D.W. / Borek, D. / Amarasinghe, G.K.
CitationJournal: Cell Rep / Year: 2014
Title: The Marburg Virus VP24 Protein Interacts with Keap1 to Activate the Cytoprotective Antioxidant Response Pathway.
Authors: Edwards, M.R. / Johnson, B. / Mire, C.E. / Xu, W. / Shabman, R.S. / Speller, L.N. / Leung, D.W. / Geisbert, T.W. / Amarasinghe, G.K. / Basler, C.F.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-associated protein VP24
B: Membrane-associated protein VP24


Theoretical massNumber of molelcules
Total (without water)51,8422
Polymers51,8422
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-11 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.775, 71.775, 191.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Membrane-associated protein VP24


Mass: 25921.072 Da / Num. of mol.: 2 / Fragment: UNP residues 11-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Gene: VP24 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05322
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 150 mM MES, pH 6.4, 20% Jeffamine M-600, pH 7.0, 50 mM cesium chloride, 6 mM barium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9790128 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9790128 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 39161 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 31.57 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.92-1.959.70.9631100
1.95-1.999.70.8131100
1.99-2.039.70.6491100
2.03-2.079.70.5271100
2.07-2.119.70.4171100
2.11-2.169.70.3571100
2.16-2.229.70.3091100
2.22-2.289.70.2891100
2.28-2.349.70.2311100
2.34-2.429.70.1941100
2.42-2.519.70.1591100
2.51-2.619.70.1251100
2.61-2.729.70.1181100
2.72-2.879.60.11100
2.87-3.059.60.0851100
3.05-3.289.60.0831100
3.28-3.619.50.0751100
3.61-4.149.40.0671100
4.14-5.219.20.0491100
5.21-508.60.051199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D9O

4d9o


Resolution: 1.921→33.597 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 1959 5.01 %
Rwork0.2095 --
obs0.2107 39067 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.5979 Å2
Refinement stepCycle: LAST / Resolution: 1.921→33.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 0 170 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013608
X-RAY DIFFRACTIONf_angle_d1.5344892
X-RAY DIFFRACTIONf_dihedral_angle_d15.41334
X-RAY DIFFRACTIONf_chiral_restr0.065573
X-RAY DIFFRACTIONf_plane_restr0.008612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.921-1.96930.29061430.26292574X-RAY DIFFRACTION100
1.9693-2.02260.28581330.24222614X-RAY DIFFRACTION100
2.0226-2.08210.24431400.23162604X-RAY DIFFRACTION100
2.0821-2.14930.24911130.2152629X-RAY DIFFRACTION100
2.1493-2.22610.25931420.21952588X-RAY DIFFRACTION100
2.2261-2.31520.24041440.22782626X-RAY DIFFRACTION100
2.3152-2.42050.2671300.22812613X-RAY DIFFRACTION100
2.4205-2.54810.271520.2172621X-RAY DIFFRACTION100
2.5481-2.70770.23761550.22512604X-RAY DIFFRACTION100
2.7077-2.91670.26811360.21652655X-RAY DIFFRACTION100
2.9167-3.210.25231500.22112649X-RAY DIFFRACTION100
3.21-3.6740.21341330.19792700X-RAY DIFFRACTION100
3.674-4.62690.19851520.18532726X-RAY DIFFRACTION100
4.6269-33.60250.20961360.20332905X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -6.9455 Å / Origin y: -13.3729 Å / Origin z: -37.2174 Å
111213212223313233
T0.1954 Å2-0.0005 Å20.0231 Å2-0.1612 Å20.0306 Å2--0.2387 Å2
L1.5397 °20.4596 °22.2643 °2-0.3784 °20.8731 °2--4.1567 °2
S-0.0226 Å °-0.1065 Å °-0.0181 Å °-0.0176 Å °0.0085 Å °0.0595 Å °0.0169 Å °-0.1888 Å °-0.1018 Å °
Refinement TLS groupSelection details: all

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