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- PDB-4ldi: Low resolution structure of Ebola virus M241R mutant -

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Basic information

Entry
Database: PDB / ID: 4ldi
TitleLow resolution structure of Ebola virus M241R mutant
ComponentsMatrix protein VP40
KeywordsVIRAL PROTEIN / ebolavirus matrix protein
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 / symbiont-mediated perturbation of host cell cycle progression / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane ...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 / symbiont-mediated perturbation of host cell cycle progression / 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 / membrane raft / ribonucleoprotein complex / 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 speciesEbola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.15 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

Downloads & links

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Assembly

Deposited unit
A: Matrix protein VP40
B: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)64,5402
Polymers64,5402
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-11 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.895, 143.895, 82.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 44:194 or resseq 201:221 or resseq...
211chain 'B' and (resseq 44:194 or resseq 201:221 or resseq...

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Components

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


Mass: 32270.207 Da / Num. of mol.: 2 / Fragment: UNP residues 44-326 / Mutation: M241R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Gene: VP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05128

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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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, 20% PEG3350, 5% dextran sulfate sodium salt (Mr = 5 kDa), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2012
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 4.15→101.749 Å / Num. all: 6959 / Num. obs: 6895 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellHighest resolution: 4.15 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1150)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.15→39.791 Å / SU ML: 0.65 / σ(F): 1.35 / Phase error: 41.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3748 331 4.81 %RANDOM
Rwork0.3116 ---
obs0.3144 6880 99.05 %-
all-6920 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.15→39.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 0 0 3732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053822
X-RAY DIFFRACTIONf_angle_d1.4035236
X-RAY DIFFRACTIONf_dihedral_angle_d13.6911426
X-RAY DIFFRACTIONf_chiral_restr0.073636
X-RAY DIFFRACTIONf_plane_restr0.009668
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1847X-RAY DIFFRACTIONPOSITIONAL
12B1847X-RAY DIFFRACTIONPOSITIONAL0.008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.15-5.22670.39661590.31213213X-RAY DIFFRACTION100
5.2267-39.79330.36691720.31153336X-RAY DIFFRACTION99

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