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- PDB-4ldm: Crystal Structure of an RNA-free VP40 Octameric Ring -

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Basic information

Entry
Database: PDB / ID: 4ldm
TitleCrystal Structure of an RNA-free VP40 Octameric Ring
ComponentsMatrix protein VP40
KeywordsVIRAL PROTEIN / ebolavirus matrix protein / RNA binding ring / viral transcription regulation
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
Matrix protein VP40, N-terminal domain / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesEbola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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


Theoretical massNumber of molelcules
Total (without water)17,5021
Polymers17,5021
Non-polymers00
Water1,838102
1
A: Matrix protein VP40
x 8


Theoretical massNumber of molelcules
Total (without water)140,0178
Polymers140,0178
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area16580 Å2
ΔGint-110 kcal/mol
Surface area40150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.457, 80.457, 47.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-288-

HOH

21A-296-

HOH

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Components

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


Mass: 17502.066 Da / Num. of mol.: 1 / Fragment: UNP residues 44-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Gene: VP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05128
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M bicine, 15% PEG20000, 3% dextran sulfate sodium salt (Mr = 5 kDa), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2012
RadiationMonochromator: liquid nitrogen cooled dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→80.457 Å / Num. all: 13886 / Num. obs: 13881 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellHighest resolution: 1.85 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: 1.85→47.543 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 694 5 %RANDOM
Rwork0.1865 ---
obs0.1873 13877 99.95 %-
all-13881 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→47.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 0 102 1035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012958
X-RAY DIFFRACTIONf_angle_d1.361311
X-RAY DIFFRACTIONf_dihedral_angle_d12.847352
X-RAY DIFFRACTIONf_chiral_restr0.076158
X-RAY DIFFRACTIONf_plane_restr0.008165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.9930.23841300.22862585X-RAY DIFFRACTION100
1.993-2.19360.28711440.20882577X-RAY DIFFRACTION100
2.1936-2.5110.21211320.19462602X-RAY DIFFRACTION100
2.511-3.16350.19071530.19512621X-RAY DIFFRACTION100
3.1635-47.5590.18351350.17242798X-RAY DIFFRACTION100
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)
12.697-2.3188-0.09584.38442.70372.87610.1547-0.17710.1862-0.11780.1851-0.3789-0.05820.4798-0.48170.2196-0.0037-0.01250.1813-0.01970.298416.308929.354424.2949
25.6716-2.1947-3.08473.12452.91655.97880.0245-0.490.32040.14420.1368-0.07220.0750.1366-0.09610.24620.0068-0.01880.2170.03680.30839.552430.395730.9165
36.22440.3208-3.39032.4521-1.76398.53510.22160.242-0.0149-0.3305-0.116-0.08380.20410.4125-0.15730.21430.03990.00060.1699-0.03090.228713.058328.4814.9179
43.13470.69723.34030.83591.21173.88190.0922-2.4374-2.94711.21930.08-1.12472.4071-0.7012-0.19191.09160.15210.09550.8360.42631.04026.479112.054335.6525
56.6758-2.70054.26693.0904-0.14614.2391-0.1001-0.4162-0.429-0.63610.83790.24660.6963-0.8699-0.50320.2356-0.03190.03660.221-0.00630.29276.16122.54223.6605
62.6085-4.2138-0.1789.76462.26992.30.24090.4621-0.7261-0.337-0.08120.34750.04-0.0643-0.26770.24760.0051-0.00220.3249-0.0540.29518.931223.454611.9932
73.6898-2.72372.32253.7333-1.79476.89510.2636-0.0516-0.0031-0.22190.0989-0.37620.93630.0837-0.50320.3411-0.01710.00660.2322-0.00310.365612.550318.905427.6949
82.72740.8104-0.43442.30020.45261.0012-0.0229-0.4923-0.280.22230.1153-0.02360.02450.0898-0.20330.20860.0056-0.0110.31050.06380.34576.712326.469133.808
94.5908-4.4726-0.99896.89054.25075.06120.1005-0.65880.78020.25560.4422-1.10450.08141.076-0.84450.26370.0050.03760.3665-0.02880.491924.536728.810218.7533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 153 )
7X-RAY DIFFRACTION7chain 'A' and (resid 154 through 162 )
8X-RAY DIFFRACTION8chain 'A' and (resid 163 through 179 )
9X-RAY DIFFRACTION9chain 'A' and (resid 180 through 186 )

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