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- PDB-6g6u: The dynamic nature of the VDAC1 channels in bilayers: human VDAC1... -

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Basic information

Entry
Database: PDB / ID: 6g6u
TitleThe dynamic nature of the VDAC1 channels in bilayers: human VDAC1 at 2.7 Angstrom resolution
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsTRANSPORT PROTEIN / ion-channel / B-barrel / outer mitochondrial membrane / cytochrome c release / APOPTOSIS
Function / homology
Function and homology information


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 / neuron-neuron synaptic transmission / Mitochondrial calcium ion transport / ceramide binding / regulation of autophagy of mitochondrion / mitochondrial permeability transition pore complex / Pyruvate metabolism / Mitochondrial protein import ...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 / neuron-neuron synaptic transmission / Mitochondrial calcium ion transport / ceramide binding / regulation of autophagy of mitochondrion / mitochondrial permeability transition pore complex / Pyruvate metabolism / Mitochondrial protein import / phosphatidylcholine binding / oxysterol binding / monoatomic anion transport / pyruvate metabolic process / cholesterol binding / porin activity / pore complex / mitochondrial nucleoid / negative regulation of reactive oxygen species metabolic process / behavioral fear response / epithelial cell differentiation / PINK1-PRKN Mediated Mitophagy / learning / mitochondrial membrane / mitochondrial outer membrane / transmembrane transporter binding / Ub-specific processing proteases / membrane raft / apoptotic process / synapse / negative regulation of apoptotic process / protein kinase binding / mitochondrion / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / NITRATE ION / Voltage-dependent anion-selective channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.74 Å
AuthorsRazeto, A. / Gribbon, P. / Loew, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other private Germany
CitationJournal: To Be Published
Title: The dynamic nature of the VDAC1 channels in bilayers as revealed by two crystal structures of the human isoform in bicelles at 2.7 and 3.3 Angstrom resolution: implications for VDAC1 voltage- ...Title: The dynamic nature of the VDAC1 channels in bilayers as revealed by two crystal structures of the human isoform in bicelles at 2.7 and 3.3 Angstrom resolution: implications for VDAC1 voltage-dependent mechanism and for its oligomerization
Authors: Razeto, A. / Gribbon, P. / Loew, C.
History
DepositionApr 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,9157
Polymers63,7572
Non-polymers2,1585
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: software PISA determined the quaternary structure . Interface area A-B: 1118 ANGSTROM**2 Solvation energy A-B: -24.5 kcal/mol
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-43 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 58.150, 122.720
Angle α, β, γ (deg.)90.000, 94.030, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 2 - 283 / Label seq-ID: 2 - 283

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Voltage-dependent anion-selective channel protein 1 / hVDAC1 / Outer mitochondrial membrane protein porin 1 / Plasmalemmal porin / Porin 31HL / Porin 31HM


Mass: 31878.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VDAC1, VDAC / Plasmid: pET21a / Details (production host): C-terminal His6-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21796
#2: Chemical ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.87 Å3/Da / Density % sol: 57.13 % / Description: plates of sizes 10 x 30 x 30 micrometers
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25.5% precipitant mix 4 [25% (v/v) MPD, 25% (w/v) PEG 1000, 25% (w/v) PEG 3350], 0.06 M NH4NO3, 0.1 buffer system 1 [imidazole and MES adjusted to pH 6.5]

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 19, 2017 / Details: CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.74→122.42 Å / Num. obs: 19091 / % possible obs: 99.1 % / Redundancy: 3.195 % / Biso Wilson estimate: 60.671 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.082 / Χ2: 0.986 / Net I/σ(I): 12.16 / Num. measured all: 61005 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.74-2.813.3370.6412.014692140714060.8060.76299.9
2.81-2.893.3440.5032.574665140413950.8760.59999.4
2.89-2.973.290.4272.944326132013150.8760.5199.6
2.97-3.063.3110.3463.614307130413010.9350.41299.8
3.06-3.173.240.2574.684040125212470.9550.30799.6
3.17-3.283.2460.2035.773895121012000.9710.24399.2
3.28-3.43.1090.147.753666119011790.9870.1799.1
3.4-3.542.860.08710.33212113311230.9950.10899.1
3.54-3.72.9920.08311.633258110510890.9960.10198.6
3.7-3.883.140.0812.933244104310330.9950.09799
3.88-4.093.3410.06116.4332749879800.9970.07399.3
4.09-4.333.30.04520.8831329529490.9980.05499.7
4.33-4.633.2780.03725.328398748660.9990.04499.1
4.63-53.2750.03924.3726668268140.9990.04698.5
5-5.483.1690.04421.2424027687580.9980.05398.7
5.48-6.133.0540.04420.6220896916840.9980.05399
6.13-7.082.8070.03620.6817046226070.9990.04597.6
7.08-8.673.1060.02727.5616155325200.9990.03297.7
8.67-12.263.2910.0234.75131040139810.02399.3
12.26-122.422.9470.0240.466692442270.9990.02493

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.51 / Cor.coef. Fo:Fc: 0.527 / Cor.coef. Io to Ic: 0.534
Highest resolutionLowest resolution
Rotation3.5 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3emn

3emn


Resolution: 2.74→122.42 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.889 / SU B: 30.934 / SU ML: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.154 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2873 960 5 %RANDOM
Rwork0.2555 ---
obs0.2571 18130 99.09 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 199.06 Å2 / Biso mean: 63.365 Å2 / Biso min: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.97 Å20 Å2-0.69 Å2
2--0.54 Å20 Å2
3---3.49 Å2
Refinement stepCycle: final / Resolution: 2.74→122.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 77 10 4413
Biso mean--39.49 41.28 -
Num. residues----555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024196
X-RAY DIFFRACTIONr_angle_refined_deg2.1011.965679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3845550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.01325.276163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30515613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.819159
X-RAY DIFFRACTIONr_chiral_restr0.1370.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023157
Refine LS restraints NCS

Ens-ID: 1 / Number: 15110 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.741→2.812 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 74 -
Rwork0.29 1327 -
all-1401 -
obs--99.86 %
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)
10.616-0.02860.56250.77390.14590.6353-0.0412-0.0730.00250.0280.0393-0.00040.04580.05640.00180.26330.005-0.02760.2320.01430.003910.13160.509113.0164
20.86060.33710.95261.07260.00891.2387-0.0809-0.02090.0317-0.1120.02740.0171-0.094-0.13470.05350.29530.0493-0.0240.2275-0.04430.010136.4107-3.827848.1122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 301
2X-RAY DIFFRACTION2B2 - 301

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