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- PDB-8b3x: High resolution crystal structure of dimeric SUDV VP40 -

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Basic information

Entry
Database: PDB / ID: 8b3x
TitleHigh resolution crystal structure of dimeric SUDV VP40
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 / virus-mediated perturbation of host defense response / 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: 1.531 Å
AuthorsWerner, A.-D. / Norris, M. / Saphire, E.O. / 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 17, 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 / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene ..._entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
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)32,6041
Polymers32,6041
Non-polymers00
Water3,729207
1
A: Matrix protein VP40

A: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)65,2072
Polymers65,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1700 Å2
ΔGint-10 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.948, 90.589, 48.13
Angle α, β, γ (deg.)90, 93.92, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-234-

PRO

21A-602-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
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: 1.000009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000009 Å / Relative weight: 1
ReflectionResolution: 1.531→51.054 Å / Num. obs: 38404 / % possible obs: 96.5 % / Redundancy: 3.25 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.221 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.0183 / Rrim(I) all: 0.0336 / AbsDiff over sigma anomalous: 0.657 / Net I/σ(I): 19.58 / Num. measured all: 124804 / % possible anomalous: 84.3 / Redundancy anomalous: 1.73
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
4.156-51.0543.150.020740.3561766176196019600.999-0.2490.01350.02480.57390.81.6896.2
3.299-4.1563.170.023639.4262476247196819680.999-0.1740.01530.02820.68192.41.6697.6
2.882-3.2993.260.026437.6363116311193419340.999-0.2840.01710.03150.72892.31.6997.5
2.618-2.8823.170.028934.1861186118192819280.998-0.3350.0190.03470.74588.81.6796
2.431-2.6182.960.030329.8755775577188518850.998-0.1610.02080.03690.758811.6194.5
2.287-2.4313.140.033228.3959865986190819080.998-0.390.02230.04020.74687.11.6596.9
2.173-2.2873.220.035926.6862176217193019300.998-0.4130.02380.04320.70287.81.6996.7
2.078-2.1733.280.039324.6663426342193119310.998-0.2670.02570.04710.72386.71.7396.4
1.998-2.0783.340.043222.0464506450193119310.997-0.1370.0280.05160.69687.61.7596.9
1.929-1.9983.350.048719.1964306430191719170.997-0.1910.03160.05820.68786.81.7797
1.869-1.9293.250.057815.9362426242192019200.996-0.0590.03780.06930.65883.71.7496.5
1.816-1.86930.072212.9155345534184418440.993-0.1180.04890.08770.65874.21.6793.9
1.768-1.8163.180.086311.4861216121192419240.992-0.1340.05670.10360.63280.61.7297
1.725-1.7683.270.100410.0263946394195819580.99-0.0030.06460.11980.61381.41.7697.6
1.685-1.7253.310.12178.6263586358192019200.986-0.090.0780.1450.61581.51.7997.2
1.65-1.6853.370.15017.2864606460191919190.9830.0050.09510.17820.59482.41.8197.2
1.617-1.653.350.16846.5764166416191619160.979-0.0950.10650.19980.577811.8197.4
1.586-1.6173.390.20315.665476547193319330.9720.0110.12810.24080.58881.11.8297
1.558-1.5863.410.23474.9165026502190819080.96-0.0980.14720.27780.563811.8296.2
1.531-1.5583.410.25894.4763766376187018700.9510.1150.16190.30610.57678.31.8493.5

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20210420data processing
XDSFeb 5, 2021data reduction
Aimless0.7.7data scaling
TRUNCATE7.1.015data processing
BUSTER2.10.4refinement
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LD8

4ld8


Resolution: 1.531→51.05 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.094 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.078 / SU Rfree Cruickshank DPI: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 1948 -RANDOM
Rwork0.1893 ---
obs0.1902 38404 96.4 %-
Displacement parametersBiso mean: 28.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.7326 Å20 Å22.6633 Å2
2--3.7092 Å20 Å2
3----0.9766 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.531→51.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 0 207 2187
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094120HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.077540HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1178SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes618HARMONIC5
X-RAY DIFFRACTIONt_it2067HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion294SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3320SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.51
X-RAY DIFFRACTIONt_other_torsion13.96
LS refinement shellResolution: 1.531→1.54 Å
RfactorNum. reflection% reflection
Rfree0.2432 42 -
Rwork0.188 --
obs--89.66 %
Refinement TLS params.

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)
10.55790.3086-0.05210.838-0.10430.50270.0047-0.07440.0717-0.0744-0.0083-0.03560.0717-0.03560.00360.006-0.0106-0.0142-0.02110.00360.0008-13.5998-20.35217.4677
21.0919-1.28911.65510.0138-0.44290.85060.0251-0.03730.0692-0.03730.0366-0.14240.0692-0.1424-0.0617-0.0381-0.01020.0073-0.01750.0166-0.0477-20.4293-5.30136.3075
31.5231-1.25981.35371.345-1.74362.52170.0727-0.18760.2269-0.1876-0.0644-0.05120.2269-0.0512-0.0082-0.0122-0.0039-0.0022-0.02370.0224-0.0433-14.3095-2.7067-2.7044
40.4616-0.26960.08061.1529-0.14460.60910.1712-0.36110.1023-0.3611-0.0161-0.3180.1023-0.318-0.1551-0.0989-0.0273-0.0428-0.05510.0217-0.1088-23.9771-10.39018.4807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|44 - 185}A44 - 185
2X-RAY DIFFRACTION2{A|186 - 233}A186 - 233
3X-RAY DIFFRACTION3{A|234 - 288}A234 - 288
4X-RAY DIFFRACTION4{A|289 - 322}A289 - 322

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