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- PDB-8ayu: Crystal structure of SUDV VP40 L117A mutant -

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Basic information

Entry
Database: PDB / ID: 8ayu
TitleCrystal structure of SUDV VP40 L117A mutant
ComponentsMatrix protein VP40
KeywordsVIRAL PROTEIN / Ebola virus / SUDV / VP40 / matrix protein / dimer
Function / homology
Function and homology information


host cell endomembrane system / host cell late endosome membrane / viral budding via host ESCRT complex / endomembrane system / structural constituent of virion / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane ...host cell endomembrane system / host cell late endosome membrane / viral budding via host ESCRT complex / endomembrane system / structural constituent of virion / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane / RNA binding / plasma membrane
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
Biological speciesSudan ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWerner, A.-D. / Steinchen, W. / Werel, L. / Kowalski, K. / Essen, L.-O. / Becker, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
LOEWE Center DRUID Germany
CitationJournal: To Be Published
Title: Crystal structure of SUDV VP40 L117A mutant
Authors: Werner, A.-D. / Becker, S.
History
DepositionSep 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)32,5621
Polymers32,5621
Non-polymers00
Water2,054114
1
A: Matrix protein VP40

A: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)65,1232
Polymers65,1232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1600 Å2
ΔGint-8 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.464, 90.700, 48.380
Angle α, β, γ (deg.)90.000, 95.049, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 32561.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Gene: VP40, DF49_53412gpVP40, DH33_45403gpVP40, SEBOVgp3 / Production host: Escherichia coli (E. coli) / References: UniProt: B0LPL6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 90 mM HEPES 6.8% (v/v) ethylen glycol 15% (v/v) glycerol 17% (v/v) PEG10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000009 Å / Relative weight: 1
ReflectionResolution: 2→48.19 Å / Num. obs: 17832 / % possible obs: 98.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.47 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1328 / CC1/2: 0.956 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
BIOMOLdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LD8

4ld8


Resolution: 2→48.19 Å / SU ML: 0.169 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.0066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 892 5 %
Rwork0.17 16937 -
obs0.1712 17829 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.87 Å2
Refinement stepCycle: LAST / Resolution: 2→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 0 114 1919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691855
X-RAY DIFFRACTIONf_angle_d0.85772542
X-RAY DIFFRACTIONf_chiral_restr0.0589311
X-RAY DIFFRACTIONf_plane_restr0.0063323
X-RAY DIFFRACTIONf_dihedral_angle_d13.1308678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.23321430.16912842X-RAY DIFFRACTION98.91
2.13-2.290.19941550.17262803X-RAY DIFFRACTION97.62
2.29-2.520.21651510.17732829X-RAY DIFFRACTION98.97
2.52-2.880.23481510.18822815X-RAY DIFFRACTION98.21
2.88-3.630.2031600.17552750X-RAY DIFFRACTION96.23
3.63-48.190.16211320.15832898X-RAY DIFFRACTION98.34
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)
11.627789073351.209230792020.4226616303253.703248816550.3609072121131.37996185461-0.03879291540290.0003616249659950.084595944533-0.129986186759-0.01721436752250.3690721695590.0473247689474-0.1421257808410.06223033003280.1852708138840.01058161801640.02049907688870.2105076434550.003591135387560.209641189981-14.2252259922-20.330776425917.5987000216
26.74157221979-1.876574586521.293093485643.66822295439-2.89900641212.54824021268-0.246512794881-0.02827145305760.158993350689-0.4020832430720.3836422237250.5006960180840.0504656798922-0.314770471773-0.1614593543410.368847996996-0.0189500547617-0.06531564228670.3135673070570.05087731569030.258217866867-18.2128464181-4.972989960150.392926602915
32.09033852379-3.074969518991.137875816515.87128167203-3.624323149144.120888593520.06415030135670.05327467755320.0903006365411-0.718217352478-0.0909814752366-0.0004136540719390.174728898224-0.133765297390.02882146845630.349281701161-0.0420578647375-0.03080360292970.3258557753080.006841909705420.285867572172-15.6224815992-5.46879840674-1.03305331033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 185 )
2X-RAY DIFFRACTION2chain 'A' and (resid 186 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 308 )

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