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- PDB-4ld8: Crystal Structure of Dimeric Sudan Virus VP40 -

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Basic information

Entry
Database: PDB / ID: 4ld8
TitleCrystal Structure of Dimeric Sudan Virus VP40
ComponentsMatrix protein VP40
KeywordsVIRAL PROTEIN / viral matrix protein / matrix assembly / viral budding / viral transcription regulation
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 / ribonucleoprotein complex / host cell plasma membrane / virion membrane / RNA binding / membrane
Similarity search - Function
EV matrix protein / Matrix protein VP40, N-terminal domain / EV matrix protein fold / EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40 / Topoisomerase I; domain 3 / Distorted Sandwich ...EV matrix protein / Matrix protein VP40, N-terminal domain / EV matrix protein fold / EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40 / Topoisomerase I; domain 3 / Distorted Sandwich / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSudan ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBornholdt, Z.A. / Ableson, D.M. / Saphire, E.O.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Structural Rearrangement of Ebola Virus VP40 Begets Multiple Functions in the Virus Life Cycle.
Authors: Bornholdt, Z.A. / Noda, T. / Abelson, D.M. / Halfmann, P. / Wood, M.R. / Kawaoka, Y. / Saphire, E.O.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
Water2,432135
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_656-x+1,y,-z+11
Buried area1690 Å2
ΔGint-10 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.364, 91.494, 48.021
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

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Components

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


Mass: 32603.617 Da / Num. of mol.: 1 / Fragment: UNP residues 44-326
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 / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG400, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator: LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.83→33.034 Å / Num. all: 23931 / Num. obs: 23880 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 1.83 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1389)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→33.034 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 1219 5.1 %RANDOM
Rwork0.1827 ---
obs0.1841 23880 99.4 %-
all-23931 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→33.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 0 135 1955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081863
X-RAY DIFFRACTIONf_angle_d1.1842539
X-RAY DIFFRACTIONf_dihedral_angle_d14.095701
X-RAY DIFFRACTIONf_chiral_restr0.076305
X-RAY DIFFRACTIONf_plane_restr0.005320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.90330.32341270.28682521X-RAY DIFFRACTION100
1.9033-1.98990.28151370.25022541X-RAY DIFFRACTION99
1.9899-2.09480.22371320.21442486X-RAY DIFFRACTION100
2.0948-2.2260.25511400.21092522X-RAY DIFFRACTION100
2.226-2.39780.25381480.19762506X-RAY DIFFRACTION100
2.3978-2.6390.23571210.1982550X-RAY DIFFRACTION100
2.639-3.02070.23741610.19422494X-RAY DIFFRACTION100
3.0207-3.80480.2011270.17682539X-RAY DIFFRACTION100
3.8048-33.03920.16181260.15352502X-RAY DIFFRACTION97
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)
11.71170.74560.43952.80340.17131.5748-0.0492-0.0110.0792-0.1264-0.01750.31710.0656-0.13970.07380.23850.0039-0.01360.2187-0.00640.234816.895724.819517.4105
22.21990.05970.27431.25560.03321.2423-0.0524-0.4089-0.02450.1726-0.00540.5575-0.2475-0.48640.07760.40030.0662-0.06320.47550.08730.507311.514440.28413.9637
31.5333-0.8343-0.06633.0703-1.24141.8330.00850.34640.1404-0.5753-0.01770.16740.1615-0.1274-0.00990.4687-0.0302-0.08250.3980.05340.364115.162540.3573-2.1067
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 308 )

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