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- PDB-8b1p: Crystal structure of SUDV VP40 CCS mutant -

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Basic information

Entry
Database: PDB / ID: 8b1p
TitleCrystal structure of SUDV VP40 CCS 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 / structural constituent of virion / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / host cell plasma membrane / virion membrane / RNA binding / 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: 1.7 Å
AuthorsWerner, A.-D. / Becker, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
LOEWE Center DRUID Germany
CitationJournal: Structure / Year: 2023
Title: The C-terminus of Sudan ebolavirus VP40 contains a functionally important CX n C motif, a target for redox modifications.
Authors: Werner, A.D. / Schauflinger, M. / Norris, M.J. / Kluver, M. / Trodler, A. / Herwig, A. / Brandstadter, C. / Dillenberger, M. / Klebe, G. / Heine, A. / Saphire, E.O. / Becker, K. / Becker, S.
History
DepositionSep 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Sep 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)32,5711
Polymers32,5711
Non-polymers00
Water2,630146
1
A: Matrix protein VP40

A: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)65,1432
Polymers65,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1680 Å2
ΔGint-10 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.851, 91.068, 48.381
Angle α, β, γ (deg.)90.000, 96.084, 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: 32571.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Strain: Human/Uganda/Gulu/2000 / Gene: VP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5XX06
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus A7 30% (w/v) GOL_4P4K (glycerol and PEG4000) 0.1 M morpheus buffer 2 (HEPES and MOPS) 60 mM morpheus divalents (MgCl2, CaCl2)

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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 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 1.6→48.11 Å / Num. obs: 35310 / % possible obs: 98.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 26.9 Å2 / CC1/2: 0.999 / Net I/σ(I): 19
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1709 / CC1/2: 0.972 / % possible all: 95.8

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Processing

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

4ld8


Resolution: 1.7→48.11 Å / SU ML: 0.1767 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.0814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2049 1512 5.09 %
Rwork0.1764 28189 -
obs0.1778 29701 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.94 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 0 146 1935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911847
X-RAY DIFFRACTIONf_angle_d1.02022531
X-RAY DIFFRACTIONf_chiral_restr0.0728310
X-RAY DIFFRACTIONf_plane_restr0.0083320
X-RAY DIFFRACTIONf_dihedral_angle_d12.1406683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.22061390.19942548X-RAY DIFFRACTION98.32
1.75-1.820.26251270.18912535X-RAY DIFFRACTION97.05
1.82-1.890.21421340.18272481X-RAY DIFFRACTION95.72
1.89-1.980.20981300.17042600X-RAY DIFFRACTION99.06
1.98-2.080.19151300.16812569X-RAY DIFFRACTION99.08
2.08-2.210.18651530.18032580X-RAY DIFFRACTION99.09
2.21-2.380.20491190.18382605X-RAY DIFFRACTION99.02
2.38-2.620.22081400.19472500X-RAY DIFFRACTION96.24
2.62-30.2361620.19412558X-RAY DIFFRACTION99.02
3-3.780.18781440.17622603X-RAY DIFFRACTION99.35
3.78-48.110.19641340.16152610X-RAY DIFFRACTION98.14
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)
11.391460289370.8662303250490.3873773153883.298139009530.08837753033911.46717373991-0.05855798451730.00515412756270.0666839298642-0.148409315433-0.002726810124920.3906140501850.0317839078598-0.1466430987120.06109736505370.2831674814980.00488154416103-0.05890406496840.180144475637-0.006263637126240.242124025699-14.6483444908-20.474330589417.5192467761
27.384431023971.05608067535-0.01347310824880.5485348492630.05381180603992.246197800350.212343065719-0.932681556972-0.0989217609671-0.152002987609-0.02181757259350.374045861839-0.276598715981-0.723469822374-0.1815421540150.4352666996650.0649138141569-0.1578373226790.4548854484030.1381623665030.420912432633-19.7502965879-4.912492106774.19848088284
32.20434866433-1.882636864891.081457813445.49040259804-2.375949369773.76182338096-0.02738352230810.1976316484150.208180813072-0.7345067695340.06399895665280.3185340842230.199280041704-0.240964620694-0.01507112165120.486510152152-0.0465929261084-0.1671730805940.3185805820230.0488383648070.345719610915-16.2401989781-5.14896564895-2.21077441351
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 235 )
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 307 )

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