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- PDB-8ayt: Crystal structure of SUDV VP40 W95A mutant -

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Basic information

Entry
Database: PDB / ID: 8ayt
TitleCrystal structure of SUDV VP40 W95A 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 / ribonucleoprotein complex / 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 / molecular replacement / Resolution: 1.9 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 W95A 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

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Assembly

Deposited unit
A: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)32,4881
Polymers32,4881
Non-polymers00
Water2,180121
1
A: Matrix protein VP40

A: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)64,9772
Polymers64,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1670 Å2
ΔGint-10 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.752, 91.279, 48.934
Angle α, β, γ (deg.)90.000, 96.709, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

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


Mass: 32488.484 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.: 121 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M potassium chloride 50 mM MOPS 12% (w/v) PEG4000 20% (w/v) glycerol

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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: 1.9→48.6 Å / Num. obs: 22067 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.51 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1406 / CC1/2: 0.912 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LD8

4ld8


Resolution: 1.9→45.64 Å / SU ML: 0.1813 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.1826
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1987 1092 4.95 %
Rwork0.167 20958 -
obs0.1685 22050 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.41 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 0 121 1977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661912
X-RAY DIFFRACTIONf_angle_d0.84242622
X-RAY DIFFRACTIONf_chiral_restr0.0588324
X-RAY DIFFRACTIONf_plane_restr0.0066334
X-RAY DIFFRACTIONf_dihedral_angle_d14.1318704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.27981330.21942614X-RAY DIFFRACTION98.67
1.99-2.090.24581460.17972591X-RAY DIFFRACTION99.24
2.09-2.220.19921410.17882613X-RAY DIFFRACTION98.85
2.22-2.390.24231260.17672612X-RAY DIFFRACTION98.52
2.39-2.630.2031230.18552628X-RAY DIFFRACTION99.28
2.63-3.020.22391540.19022595X-RAY DIFFRACTION99.46
3.02-3.80.20021450.17232619X-RAY DIFFRACTION98.36
3.8-45.640.16341240.14282686X-RAY DIFFRACTION99.22
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)
11.793877790021.360821745860.4752085203184.091916865080.06315286562541.36697286788-0.0584706216563-0.007868605150130.133008023984-0.141738061899-0.006861794553320.49352413022-0.00527412829792-0.1529498651110.07113374288010.2046745421440.01960799667840.001136307227260.248578156975-0.002943389113790.266679846826-15.1305669812-20.710543299717.7987863114
27.47507831688-0.499637700685-0.3613368083722.28067300801-2.10440310114.103052175080.0427983714997-0.2440803691050.512162696545-0.358391028060.1895824472080.455800029584-0.303995399038-0.535508396598-0.2098685897920.3854960526850.0560169888601-0.1243352558040.3538249142520.05579392083510.46818860166-21.8560271386-1.950111513721.26326696743
32.93572584665-4.403031437381.615574253717.07930383934-3.066715603794.957712354140.07465226809310.1521145109020.0122659357058-0.821967771027-0.107262945737-0.1859629798620.2893958658260.1027249482680.0295783481410.440109535093-0.0699592549251-0.07492807311410.3949361681960.03471872504410.332684987714-15.2842373585-7.25894184875-1.24173123907
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 246 )
3X-RAY DIFFRACTION3chain 'A' and (resid 247 through 308 )

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