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- PDB-3vnf: Structure of the ebolavirus protein VP24 from Sudan -

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Basic information

Entry
Database: PDB / ID: 3vnf
TitleStructure of the ebolavirus protein VP24 from Sudan
ComponentsMembrane-associated protein VP24
KeywordsVIRAL PROTEIN / ebolavirus / interferon antagonist / VP24 / STAT1 / Zaire / Sudan / Reston / VP35 / karyopherin alpha / IFN response pathway
Function / homology
Function and homology information


host cell endomembrane system / endomembrane system / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane / structural molecule activity / membrane / plasma membrane
Similarity search - Function
Filovirus membrane-associated VP24 / Filovirus membrane-associated protein VP24
Similarity search - Domain/homology
Membrane-associated protein VP24 / Membrane-associated protein VP24
Similarity search - Component
Biological speciesSudan ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsZhang, A.P.P.
CitationJournal: Plos Pathog. / Year: 2012
Title: The ebola virus interferon antagonist VP24 directly binds STAT1 and has a novel, pyramidal fold
Authors: Zhang, A.P.P. / Bornholdt, Z.A. / Liu, T. / Abelson, D.M. / Lee, D.E. / Li, S. / Woods Jr., V.L. / Saphire, E.O.
History
DepositionJan 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Membrane-associated protein VP24


Theoretical massNumber of molelcules
Total (without water)24,5841
Polymers24,5841
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Membrane-associated protein VP24

A: Membrane-associated protein VP24


Theoretical massNumber of molelcules
Total (without water)49,1672
Polymers49,1672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1820 Å2
ΔGint-9 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.110, 61.110, 126.820
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 Membrane-associated protein VP24 / Minor matrix protein


Mass: 24583.521 Da / Num. of mol.: 1 / Fragment: UNP residues 13-228 / Mutation: V22A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Gene: VP24 / Production host: Escherichia coli (E. coli) / References: UniProt: B0LPM0, UniProt: Q5XX02*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7855.72
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion70.1M HEPES, pH 7.0, 6% (+/-)-MPD, 15% (w/v) D-(+)-sucrose, VAPOR DIFFUSION, temperature 295K
2952vapor diffusion70.1M HEPES, pH 7.0, 10% MPD, 1mM DTT, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9794
SYNCHROTRONAPS 19-ID20.97940, 0.97951
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 30, 2010
ADSC QUANTUM 3152CCDOct 30, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystalSINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979511
ReflectionResolution: 1.8→33.03 Å / Num. all: 25038 / Num. obs: 23986 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 53.67 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.3
Reflection shellHighest resolution: 1.8 Å / % possible all: 95.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
d*TREKdata reduction
d*TREKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→33.03 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7717 / SU ML: 0.38 / σ(F): 0 / Phase error: 28.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1326 8.01 %random
Rwork0.2339 ---
all0.2368 16617 --
obs0.2368 16550 99.6 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.101 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 193.9 Å2 / Biso mean: 77.1694 Å2 / Biso min: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.034 Å20 Å2-0 Å2
2--4.034 Å20 Å2
3----8.068 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 0 46 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141700
X-RAY DIFFRACTIONf_angle_d1.1022195
X-RAY DIFFRACTIONf_chiral_restr0.069259
X-RAY DIFFRACTIONf_plane_restr0.004272
X-RAY DIFFRACTIONf_dihedral_angle_d14.395602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1002-2.18430.3671440.362616701814100
2.1843-2.28360.35421450.332216461791100
2.2836-2.4040.36111460.361616561802100
2.404-2.55460.40861490.382916811830100
2.5546-2.75170.48621490.40416671816100
2.7517-3.02850.33891450.274316861831100
3.0285-3.46630.27341420.222817001842100
3.4663-4.36560.22341510.186117481899100
4.3656-33.03380.22671550.1981770192598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29771.28560.28971.3878-0.06432.8731-0.0220.3340.1601-0.05590.2910.25230.4282-0.0672-0.24160.4056-0.0377-0.05740.4908-0.02040.38758.336318.4762-15.9044
22.35460.8437-0.90361.5926-1.06843.1415-0.00960.3712-0.0468-0.14380.0463-0.16540.56620.1295-0.0420.39440.085-0.00480.423-0.07260.328817.768415.7026-17.0393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 13:83)A13 - 83
2X-RAY DIFFRACTION2(chain A and resid 84:228)A84 - 228

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