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- PDB-9rdm: SUDV VP40 in complex with 3-aminosalicylic acid -

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Basic information

Entry
Database: PDB / ID: 9rdm
TitleSUDV VP40 in complex with 3-aminosalicylic acid
ComponentsMatrix protein VP40
KeywordsVIRAL PROTEIN / Sudan virus / SUDV / filovirus / matrix protein / VP40
Function / homology
Function and homology information


host cell endomembrane system / host cell late endosome membrane / viral budding via host ESCRT complex / structural constituent of virion / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / host cell plasma membrane / virion membrane / RNA 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
3-amino-2-hydroxybenzoic acid / Matrix protein VP40
Similarity search - Component
Biological speciesSudan ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWerner, A.-D. / Laube, L. / Diederich, W. / Becker, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
LOEWE Center DRUID Germany
CitationJournal: To Be Published
Title: SUDV VP40 in complex with 3-aminosalicylic acid
Authors: Werner, A.-D. / Laube, L. / Diederich, W. / Becker, S.
History
DepositionJun 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein VP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7572
Polymers32,6041
Non-polymers1531
Water1,910106
1
A: Matrix protein VP40
hetero molecules

A: Matrix protein VP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5144
Polymers65,2072
Non-polymers3062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1700 Å2
ΔGint-10 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.741, 90.640, 48.313
Angle α, β, γ (deg.)90.000, 94.330, 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 / Ebola VP40 / eVP40 / Membrane-associated protein VP40


Mass: 32603.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Gene: VP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5XX06
#2: Chemical ChemComp-1CW / 3-amino-2-hydroxybenzoic acid


Mass: 153.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES; 40 mM MgCl2; 10% (v/v) PEG400; 20% ethylen glycol as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 1.48→34.13 Å / Num. obs: 31769 / % possible obs: 98 % / Redundancy: 3.2 % / Biso Wilson estimate: 24.87 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.66
Reflection shellResolution: 1.48→1.536 Å / Redundancy: 2.4 % / Num. unique obs: 3883 / CC1/2: 0.511 / % possible all: 86.42

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→34.13 Å / SU ML: 0.1846 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7017
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2189 1543 4.86 %
Rwork0.1931 30207 -
obs0.1947 31747 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.13 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 11 106 1960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611930
X-RAY DIFFRACTIONf_angle_d0.87272653
X-RAY DIFFRACTIONf_chiral_restr0.0581324
X-RAY DIFFRACTIONf_plane_restr0.0073338
X-RAY DIFFRACTIONf_dihedral_angle_d11.9479702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.33071480.24852713X-RAY DIFFRACTION97.11
1.7-1.760.27271260.23052712X-RAY DIFFRACTION97.09
1.76-1.830.25581610.22532675X-RAY DIFFRACTION96.04
1.83-1.920.24471310.21712724X-RAY DIFFRACTION97.61
1.92-2.020.22491490.19842763X-RAY DIFFRACTION99.39
2.02-2.150.22391340.18792775X-RAY DIFFRACTION99.42
2.15-2.310.23331480.20582774X-RAY DIFFRACTION98.78
2.31-2.540.24431230.2162750X-RAY DIFFRACTION97.85
2.54-2.910.22611450.20852731X-RAY DIFFRACTION97.96
2.91-3.670.20711450.19282793X-RAY DIFFRACTION99.32
3.67-34.130.19291330.16812797X-RAY DIFFRACTION97.7

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