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- PDB-7tcv: VDAC K12E mutant -

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Basic information

Entry
Database: PDB / ID: 7tcv
TitleVDAC K12E mutant
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsMEMBRANE PROTEIN / Voltage-dependent ion channel / VDAC
Function / homology
Function and homology information


Pyruvate metabolism / negative regulation of calcium import into the mitochondrion / positive regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / voltage-gated monoatomic anion channel activity / PINK1-PRKN Mediated Mitophagy / neuron-neuron synaptic transmission / mitochondrial calcium ion transmembrane transport / acetyl-CoA biosynthetic process from pyruvate / ceramide binding / monoatomic anion channel activity ...Pyruvate metabolism / negative regulation of calcium import into the mitochondrion / positive regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / voltage-gated monoatomic anion channel activity / PINK1-PRKN Mediated Mitophagy / neuron-neuron synaptic transmission / mitochondrial calcium ion transmembrane transport / acetyl-CoA biosynthetic process from pyruvate / ceramide binding / monoatomic anion channel activity / regulation of mitophagy / mitochondrial permeability transition pore complex / phosphatidylcholine binding / Ub-specific processing proteases / oxysterol binding / cholesterol binding / porin activity / mitochondrial nucleoid / negative regulation of reactive oxygen species metabolic process / behavioral fear response / presynaptic active zone membrane / epithelial cell differentiation / learning / postsynaptic density membrane / synaptic vesicle / myelin sheath / chemical synaptic transmission / mitochondrial outer membrane / transmembrane transporter binding / mitochondrial inner membrane / membrane raft / nucleotide binding / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / membrane / identical protein binding / plasma membrane
Similarity search - Function
Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Voltage-dependent anion-selective channel protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsKhan, F. / Abramson, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Dynamical control of the mitochondrial beta-barrel channel VDAC by electrostatic and mechanical coupling
Authors: Ngo, V.A. / Martin, M.Q. / Khan, F. / Bergdoll, L. / Abramson, J. / Bezrukov, S.M. / Rostovtseva, T.K. / Hoogerheide, D.P. / Noskov, S.Y.
History
DepositionDec 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
XXX: Voltage-dependent anion-selective channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8742
Polymers32,1961
Non-polymers6781
Water84747
1
XXX: Voltage-dependent anion-selective channel protein 1
hetero molecules

XXX: Voltage-dependent anion-selective channel protein 1
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 65.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)65,7484
Polymers64,3922
Non-polymers1,3562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3080 Å2
ΔGint-40 kcal/mol
Surface area30770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.197, 57.800, 66.440
Angle α, β, γ (deg.)90.000, 97.664, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Voltage-dependent anion-selective channel protein 1 / mVDAC1 / Outer mitochondrial membrane protein porin 1 / Plasmalemmal porin / Voltage-dependent ...mVDAC1 / Outer mitochondrial membrane protein porin 1 / Plasmalemmal porin / Voltage-dependent anion-selective channel protein 5 / mVDAC5


Mass: 32195.879 Da / Num. of mol.: 1 / Mutation: K12E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vdac1, Vdac5 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: Q60932
#2: Chemical ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 8.5, 10% Polyethylene glycol (PEG) 400 and 16% 2-Methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.6→49.745 Å / Num. obs: 11349 / % possible obs: 99 % / Redundancy: 9.8 % / CC1/2: 0.99 / Net I/σ(I): 18.7
Reflection shellResolution: 2.6→2.72 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1290 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EMN

3emn


Resolution: 2.604→49.745 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 10.95 / SU ML: 0.238 / Cross valid method: FREE R-VALUE / ESU R: 0.59 / ESU R Free: 0.33
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2766 571 5.032 %
Rwork0.2175 10777 -
all0.22 --
obs-11348 98.893 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.627 Å2
Baniso -1Baniso -2Baniso -3
1-0.585 Å2-0 Å2-0.296 Å2
2--2.414 Å20 Å2
3----2.817 Å2
Refinement stepCycle: LAST / Resolution: 2.604→49.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 21 47 2165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132164
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171935
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.6462934
X-RAY DIFFRACTIONr_angle_other_deg1.2351.5774485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0315284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89924.19493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.11615333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.253156
X-RAY DIFFRACTIONr_chiral_restr0.0580.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
X-RAY DIFFRACTIONr_nbd_refined0.1910.2325
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21697
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2977
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21192
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.277
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.210
X-RAY DIFFRACTIONr_nbd_other0.20.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2230.21
X-RAY DIFFRACTIONr_mcbond_it4.5355.81136
X-RAY DIFFRACTIONr_mcbond_other4.5215.7971135
X-RAY DIFFRACTIONr_mcangle_it7.0368.6931420
X-RAY DIFFRACTIONr_mcangle_other7.0388.6961421
X-RAY DIFFRACTIONr_scbond_it5.6646.3961028
X-RAY DIFFRACTIONr_scbond_other5.616.3871026
X-RAY DIFFRACTIONr_scangle_it8.5879.3571514
X-RAY DIFFRACTIONr_scangle_other8.5849.3561515
X-RAY DIFFRACTIONr_lrange_it11.9167.3262183
X-RAY DIFFRACTIONr_lrange_other11.91167.3092182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.604-2.6710.35310.27714X-RAY DIFFRACTION87.7503
2.671-2.7440.337530.236755X-RAY DIFFRACTION97.9394
2.744-2.8240.253280.217756X-RAY DIFFRACTION100
2.824-2.9110.268420.216727X-RAY DIFFRACTION99.8701
2.911-3.0060.296380.208730X-RAY DIFFRACTION99.87
3.006-3.1110.289370.197655X-RAY DIFFRACTION100
3.111-3.2280.312320.203683X-RAY DIFFRACTION100
3.228-3.360.296330.182645X-RAY DIFFRACTION100
3.36-3.5090.234460.184601X-RAY DIFFRACTION100
3.509-3.6790.25350.193591X-RAY DIFFRACTION100
3.679-3.8780.299420.236546X-RAY DIFFRACTION100
3.878-4.1120.265290.232541X-RAY DIFFRACTION100
4.112-4.3950.204250.194505X-RAY DIFFRACTION100
4.395-4.7450.218210.179470X-RAY DIFFRACTION99.7967
4.745-5.1950.222190.196442X-RAY DIFFRACTION100
5.195-5.8040.302210.227383X-RAY DIFFRACTION100
5.804-6.6930.329120.297346X-RAY DIFFRACTION100
6.693-8.1770.37570.254318X-RAY DIFFRACTION100
8.177-11.4750.387120.224235X-RAY DIFFRACTION100
11.475-49.7450.36780.297134X-RAY DIFFRACTION98.6111

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