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- PDB-7jzj: Crystal structure demonstrating CTD-CTD interactions of Zaire Ebo... -

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Basic information

Entry
Database: PDB / ID: 7jzj
TitleCrystal structure demonstrating CTD-CTD interactions of Zaire Ebola virus VP40 dimer
ComponentsMatrix protein VP40
KeywordsVIRAL PROTEIN / VP40 / matrix protein / Ebola virus
Function / homology
Function and homology information


intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane / host cell ...intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane / host cell / structural constituent of virion / ribonucleoprotein complex / membrane raft / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane / RNA binding / extracellular region / identical protein 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
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsNorris, M.J. / Bornholdt, Z.A. / Saphire, E.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI118016 United States
CitationJournal: Elife / Year: 2020
Title: Ebola and Marburg virus matrix layers are locally ordered assemblies of VP40 dimers.
Authors: William Wan / Mairi Clarke / Michael J Norris / Larissa Kolesnikova / Alexander Koehler / Zachary A Bornholdt / Stephan Becker / Erica Ollmann Saphire / John Ag Briggs /
Abstract: Filoviruses such as Ebola and Marburg virus bud from the host membrane as enveloped virions. This process is achieved by the matrix protein VP40. When expressed alone, VP40 induces budding of ...Filoviruses such as Ebola and Marburg virus bud from the host membrane as enveloped virions. This process is achieved by the matrix protein VP40. When expressed alone, VP40 induces budding of filamentous virus-like particles, suggesting that localization to the plasma membrane, oligomerization into a matrix layer, and generation of membrane curvature are intrinsic properties of VP40. There has been no direct information on the structure of VP40 matrix layers within viruses or virus-like particles. We present structures of Ebola and Marburg VP40 matrix layers in intact virus-like particles, and within intact Marburg viruses. VP40 dimers assemble extended chains via C-terminal domain interactions. These chains stack to form 2D matrix lattices below the membrane surface. These lattices form a patchwork assembly across the membrane and suggesting that assembly may begin at multiple points. Our observations define the structure and arrangement of the matrix protein layer that mediates formation of filovirus particles.
History
DepositionSep 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein VP40
B: Matrix protein VP40
C: Matrix protein VP40
D: Matrix protein VP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,6317
Polymers128,9174
Non-polymers7153
Water1,24369
1
A: Matrix protein VP40
D: Matrix protein VP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9354
Polymers64,4582
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Matrix protein VP40
C: Matrix protein VP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6973
Polymers64,4582
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.940, 159.940, 89.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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Components

#1: Protein
Matrix protein VP40 / Ebola VP40 / eVP40 / Membrane-associated protein VP40


Mass: 32229.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: VP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05128
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.05 M magnesium chloride, 0.1 M HEPES, 38% PEG400, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 85 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2010
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.46→79.97 Å / Num. obs: 44360 / % possible obs: 93.1 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.037 / Rrim(I) all: 0.105 / Net I/σ(I): 15.3 / Num. measured all: 350132
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.46-2.5983.3685543769040.4431.2613.5980.999.8
7.78-79.977.40.02111710158410.0080.02368.599.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
Coot0.9 ELmodel building
PHASER1.17.1_3660phasing
Aimless0.7.4data scaling
XDSJan 31, 2020data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LDB

4ldb


Resolution: 2.46→46.17 Å / SU ML: 0.4135 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.8484
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 2185 5 %
Rwork0.2492 41496 -
obs0.2497 43681 91.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.14 Å2
Refinement stepCycle: LAST / Resolution: 2.46→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7330 0 48 69 7447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01347561
X-RAY DIFFRACTIONf_angle_d1.949810375
X-RAY DIFFRACTIONf_chiral_restr0.10081262
X-RAY DIFFRACTIONf_plane_restr0.00791339
X-RAY DIFFRACTIONf_dihedral_angle_d19.14421049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.510.40591570.41892468X-RAY DIFFRACTION88.8
2.51-2.570.44341720.40492665X-RAY DIFFRACTION95.78
2.57-2.640.38071260.38642780X-RAY DIFFRACTION98.34
2.64-2.710.3884630.37871370X-RAY DIFFRACTION48.3
2.71-2.790.40911480.35942802X-RAY DIFFRACTION99.63
2.79-2.880.32621160.3352816X-RAY DIFFRACTION99.66
2.88-2.980.3341280.33272846X-RAY DIFFRACTION99.73
2.98-3.10.29751420.30782821X-RAY DIFFRACTION99.93
3.1-3.240.32021530.29972789X-RAY DIFFRACTION99.59
3.24-3.40.28811390.29232695X-RAY DIFFRACTION99.44
3.46-3.620.2951280.26372083X-RAY DIFFRACTION99.73
3.62-3.860.3082910.25072086X-RAY DIFFRACTION84.25
3.92-4.30.21341620.20382683X-RAY DIFFRACTION99.61
4.3-4.920.17721540.18912836X-RAY DIFFRACTION100
4.92-6.190.22061740.21762822X-RAY DIFFRACTION99.93
6.19-46.170.24261320.22682934X-RAY DIFFRACTION99.8
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)
16.62911503511-0.7768008775962.592688847384.5163602482-2.269170226714.88379312074-0.271073327495-0.5340036203650.3756588716820.292494199811-0.139631246414-0.7038119714960.1742498729850.5250581948790.344104556780.889132165595-0.145113571616-0.04284429067880.776660010299-0.00369501606780.595433271176-32.493244938331.665221930355.3342451878
24.28698679939-0.3502332308432.191246438090.802240636816-0.930019301686.544198881670.152531413191-0.04230127938710.213105496683-0.102631119897-0.5868328525940.3823492701750.1358650417241.862676675560.5160057623091.20712097702-0.246641150597-0.09379962115391.028357199220.1017827301450.942932141047-44.323863100624.961105888556.5843833236
33.71273046892-2.460112680270.3143874842784.063236818210.0298355775133.444569406020.1797328358260.1726939068820.226956623103-0.321488152631-0.2501013757190.2778283203050.391515948147-0.1196956633850.07680130154080.722252287347-0.21989108891-0.02408673569640.4511516554980.01023189635770.546303302636-58.763311172931.974786946519.3630166529
43.394168364230.210163481056-2.615845518724.257177187262.086764931957.601046709250.0985650190262-0.267627444454-0.342518774750.537746912306-0.3478522036470.2255379459821.21194906957-0.2409835354080.262731626561.2000621665-0.158840850216-0.1183349596450.663500322167-0.0637637943840.630161952859-60.430999615511.97187370025.6826679401
52.509950294731.1015617235-0.704024032684.379189680082.710833114935.65124256853-0.133385074804-0.0493809222459-0.295765089993-0.267023884711-0.130303724745-0.08190374392470.807633069513-0.03932662017910.2119766014620.820170914631-0.113359329251-0.1242396682350.56951192120.01025092465190.716987809486-60.739224807417.17455875028.07724044824
64.190959483-1.229616245940.009642170622482.746939726690.7416029778283.54577429845-0.209925287077-0.07875020188450.1201896363470.1529131582990.06707987483560.3248928513530.0833526046622-0.002621088389830.1346911610440.524870315131-0.0991594300471-0.01228115514290.4571168251120.02642234835420.557800935401-40.474827353553.071726286426.1433018317
75.15220766441-2.26745681721-2.068988286841.29526425419-0.6834102909949.17278789410.04216126248390.697500979061-0.6243733529740.0325549694322-0.682128932838-0.01136349003050.215926503583-0.6730024486020.5126547249640.819986845771-0.117768668855-0.1027210918690.966412968323-0.145165191710.828835908627-28.659029537952.306396480142.1245278832
86.52115635541-0.9842560554613.140301418622.64274024315-1.853927401186.75051200102-0.0224421331111-0.6385682464930.3003861458840.260616937941-0.0529101232135-0.394814768444-0.03276688635960.7648583908260.07472490823040.658201213962-0.08416447063630.00256467975280.82867892412-0.08533537631790.637553650572-22.736761154859.39508147438.9705694676
93.27176023259-0.336851097702-0.567666520553.811217190590.09622488764223.40779325366-0.3878955858830.7610275001440.388886428585-0.5675230670910.3909178840210.0198084816277-0.097513963260.216908688492-0.05324498927380.742230399535-0.285964334885-0.1385385070450.9239265897750.0965302771950.547080370869-39.851157900747.45951711190.0621997193727
105.1076538267-1.45085943067-2.141058589844.986859022610.3184189749283.63595352581-0.1683025945390.320801856584-0.424098470201-0.360447040334-0.1386326603220.134788960421.15519602477-0.08738421461010.3230504220661.17089293675-0.124196583258-0.01882365833710.888721466086-0.1122221407930.670701248517-35.679631060627.2100527806-9.64408402432
112.86266529103-1.40013542432-0.3049340922774.662939892933.874151122353.64331120699-0.1694795234861.191926302120.3764703221930.738798795765-0.30431598328-0.2628450629441.874596520930.9653333734080.5311023654931.31903356623-0.3230798533750.1542751220431.376017906790.1282710725430.591400864588-32.701809727239.3098167528-10.2441022386
123.76689728966-1.26044817919-0.4110461915493.429055570950.499795236215.6671792745-0.0333968925957-0.331659290114-0.04878331690230.3186715780580.01742074142420.3564832404530.269183626253-0.1055880178620.03817637482140.874854927815-0.1856042192750.06941332819220.525858824803-0.01507877904690.57046205186-53.120004080132.433739214245.9130195002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain D and resid 192:307)
2X-RAY DIFFRACTION2(chain D and resid 308:324)
3X-RAY DIFFRACTION3(chain A and resid 43:191)
4X-RAY DIFFRACTION4(chain A and resid 192:273)
5X-RAY DIFFRACTION5(chain A and resid 274:316)
6X-RAY DIFFRACTION6(chain B and resid 44:193)
7X-RAY DIFFRACTION7(chain B and resid 194:214)
8X-RAY DIFFRACTION8(chain B and resid 215:321)
9X-RAY DIFFRACTION9(chain C and resid 45:188)
10X-RAY DIFFRACTION10(chain C and resid 189:308)
11X-RAY DIFFRACTION11(chain C and resid 309:322)
12X-RAY DIFFRACTION12(chain D and resid 45:191)

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