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- PDB-3emn: The Crystal Structure of Mouse VDAC1 at 2.3 A resolution -

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Basic information

Entry
Database: PDB / ID: 3emn
TitleThe Crystal Structure of Mouse VDAC1 at 2.3 A resolution
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsMEMBRANE PROTEIN / VDAC1 / Eukaryotic Membrane Protein / Beta Barrel / Channel / Apoptosis / Ion transport / Mitochondrion / Outer membrane / Phosphoprotein / Porin / Transmembrane / Transport
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 / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
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 / SIRAS / Resolution: 2.3 Å
AuthorsUjwal, R. / Cascio, D. / Colletier, J.-P. / Faham, S. / Zhang, J. / Toro, L. / Ping, P. / Abramson, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: The crystal structure of mouse VDAC1 at 2.3 A resolution reveals mechanistic insights into metabolite gating
Authors: Ujwal, R. / Cascio, D. / Colletier, J.P. / Faham, S. / Zhang, J. / Toro, L. / Ping, P. / Abramson, J.
History
DepositionSep 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,8742
Polymers32,1961
Non-polymers6781
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
X: Voltage-dependent anion-selective channel protein 1
hetero molecules

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


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 area3220 Å2
ΔGint-44 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.230, 58.390, 66.580
Angle α, β, γ (deg.)90.000, 99.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 32195.945 Da / Num. of mol.: 1 / Fragment: sequence database residues 14-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vdac1, Vdac5 / Plasmid: pQE9 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / 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

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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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18% MPD, 0.1 M Tris-HCl, 10% PEG400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.9792
SYNCHROTRONALS 5.0.221
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJun 23, 2008Mirror
ADSC QUANTUM 3152CCDAug 30, 2008Mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryogenically-cooled single crystal Si(111) side bounce monochromatorSINGLE WAVELENGTHMx-ray1
2double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
211
ReflectionRedundancy: 2.8 % / Number: 44352 / Rmerge(I) obs: 0.088 / Χ2: 1.9 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 16051 / % possible obs: 98.8
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
6.245017898.70.0573.1362.8
4.966.2475499.90.0873.2942.9
4.334.96223799.90.0753.0922.9
3.944.33154299.90.0812.0912.9
3.653.949081000.0971.6722.9
3.443.65116399.90.1091.3942.9
3.273.4414801000.1421.0872.9
3.123.2720141000.2070.9312.8
33.12122399.90.2840.7952.7
2.93144089.50.2470.7511.9
ReflectionResolution: 2.3→19.51 Å / Num. obs: 16629 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 48.726 Å2 / Rmerge(I) obs: 0.029
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 6493 / Num. unique all: 2010 / Num. unique obs: 2010 / % possible all: 98.7

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Phasing

PhasingMethod: SIRAS
Phasing MADD res high: 3 Å / D res low: 66.23 Å / FOM : 0.418 / FOM acentric: 0.396 / FOM centric: 0.706 / Reflection: 7794 / Reflection acentric: 7242 / Reflection centric: 552
Phasing MAD setR cullis acentric: 0.75 / R cullis centric: 0.68 / Highest resolution: 3 Å / Lowest resolution: 66.23 Å / Loc acentric: 39.9 / Loc centric: 57.1 / Power acentric: 1.96 / Power centric: 1.61 / Reflection acentric: 7242 / Reflection centric: 552
Phasing MAD set shell

ID: 1

Resolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
18.22-66.230.710.5684.9145.52.051.45166
10.56-18.220.580.4962.1762.852.312226
7.44-10.560.620.6845.769.63.382.1929144
5.74-7.440.60.7141.558.13.232.2856067
4.67-5.740.770.654.663.51.981.6887879
3.94-4.670.80.7453.668.11.591.29126993
3.41-3.940.780.7638.351.61.661.241782110
3-3.410.80.7225.436.71.781.242324127
Phasing MAD set siteAtom type symbol: Hg / B iso: 53.669 / Fract x: 0.288 / Fract y: 0.583 / Fract z: 0.168 / Occupancy: 1
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
18.22-66.230.5570.4360.88122166
10.56-18.220.5860.5560.72514812226
7.44-10.560.6120.5890.75833529144
5.74-7.440.5550.5290.77862756067
4.67-5.740.4540.4330.68995787879
3.94-4.670.4080.3910.6371362126993
3.41-3.940.3940.3760.69218921782110
3-3.410.3550.3350.71124512324127
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 7802
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.5-10046.40.837503
5.95-7.551.50.847505
5.21-5.9552.40.812504
4.74-5.2157.30.831501
4.39-4.74590.825506
4.12-4.3962.70.697516
3.91-4.12710.592506
3.74-3.9165.50.665506
3.59-3.7467.30.628502
3.47-3.5974.30.652509
3.36-3.4777.90.638510
3.26-3.3675.90.607501
3.18-3.2679.10.584501
3.1-3.1875.30.542503
2.95-3.181.60.473729

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→19.51 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.298 / WRfactor Rwork: 0.266 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.771 / SU B: 15.381 / SU ML: 0.192 / SU R Cruickshank DPI: 0.368 / SU Rfree: 0.275 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.33 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 843 5.1 %RANDOM
Rwork0.242 ---
obs0.244 16629 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.81 Å2 / Biso mean: 48.473 Å2 / Biso min: 21.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.13 Å2
2--0.11 Å20 Å2
3---0.5 Å2
Refine analyzeLuzzati coordinate error free: 0.247 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 22 47 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222246
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9563034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7155284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.64325.15597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.45115376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.622157
X-RAY DIFFRACTIONr_chiral_restr0.1210.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021685
X-RAY DIFFRACTIONr_mcbond_it0.8311.51395
X-RAY DIFFRACTIONr_mcangle_it1.58322228
X-RAY DIFFRACTIONr_scbond_it2.2593851
X-RAY DIFFRACTIONr_scangle_it3.8124.5806
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 59 -
Rwork0.294 1175 -
all-1234 -
obs--98.64 %
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)
10.2293-0.83040.66586.378-1.25682.32850.0242-0.19860.134-0.49290.2260.49030.4579-0.009-0.2502-0.12390.03380.0102-0.1277-0.0163-0.122512.100631.772426.2802
20.4643-0.5205-0.13244.07583.19592.69710.19030.3783-0.0923-0.2060.1193-0.28250.332-0.3185-0.3096-0.0328-0.07210.00540.06210.0437-0.07959.937441.94678.2219
30.09320.4514-0.51653.9356-0.75384.61040.26950.0972-0.61850.9895-0.2365-0.1775-0.6241-0.5615-0.0330.04130.0483-0.02520.22640.08720.1163-4.684427.492810.2289
45.85335.1244-2.20444.9168-1.43491.88850.0415-0.03310.0622-0.0037-0.01260.0371-0.13160.0468-0.0289-0.02150.0378-0.01380.03020.0250.01737.460233.91771.4436
53.62094.7125-3.85176.1921-4.72255.52480.0123-0.0545-0.0159-0.069-0.0295-0.02350.068-0.07960.0172-0.03020.04220.00060.04360.00840.04571.815922.11377.3764
60.64380.8068-1.92252.4945-2.45266.01130.04940.0708-0.0378-0.15630.005-0.04050.03990.0491-0.0544-0.03240.0277-0.00270.0452-0.00650.0186.384817.82736.5715
72.9258-0.06850.18481.46481.52753.8509-0.039-0.0871-0.08160.08180.01130.04620.065-0.14370.0277-0.0071-0.0088-0.00640.0218-0.0037-0.00172.473911.284324.0777
80.76070.57-1.77071.145-1.39945.9989-0.02860.1964-0.0478-0.1518-0.0619-0.1327-0.0073-0.08950.09050.0070.0233-0.01960.04260.02020.035513.09214.7749.6858
92.3197-0.3614-0.66352.24321.14791.1905-0.04420.2227-0.0465-0.09430.1527-0.0463-0.02880.079-0.1085-0.04760.0259-0.0204-0.13360.067-0.105616.961718.964125.9752
105.5153-2.08490.9416.94774.11143.4002-0.00760.3497-0.5852-0.0658-0.0275-0.314-0.10990.34640.03510.01640.00840.0258-0.00510.02320.037131.009115.67818.8913
117.1483-4.4898-3.60145.88311.2023.25530.02760.1932-0.12490.1573-0.07310.01260.0735-0.10290.0455-0.0942-0.0234-0.0626-0.1052-0.0265-0.147920.282131.979430.1336
125.3798-2.02370.82412.7223-0.11631.0349-0.0117-0.28590.08120.03610.08570.0712-0.1445-0.1586-0.074-0.0177-0.01920.001-0.0813-0.0137-0.09612.038442.391628.8188
135.9746-1.71040.69072.48920.11321.75360.0990.3623-0.2937-0.11840.0239-0.2487-0.28480.0384-0.1229-0.0518-0.02230.0495-0.1414-0.0298-0.165923.827443.203425.7937
144.01850.03671.19390.19250.02920.6206-0.08460.03970.01930.0040.05990.0991-0.0407-0.08330.02470.00760.00290.0153-0.0321-0.0046-0.03229.018547.837921.4613
155.697-0.00861.01810.422-0.02350.49930.0009-0.11960.1041-0.03770.00020.05250.0106-0.035-0.0011-0.0057-0.00510.0152-0.02230.0042-0.042113.44549.827817.9061
166.94881.49280.77511.08080.20950.87640.02880.02510.15350.0409-0.03050.0835-0.0509-0.01340.00170.00150.01310.004-0.03520.0207-0.04249.568550.637813.3174
175.2945-0.4014-0.32210.58530.07280.81950.0171-0.00470.10630.0173-0.03350.1783-0.0596-0.04190.0164-0.00440.017-0.00090.01110.0076-0.0118-5.780443.47768.2071
183.9722.2441.1923.480.30241.074-0.01060.05030.07830.05110.02290.0456-0.13180.0503-0.01230.0081-0.00020.0065-0.00390.0077-0.03412.842150.35968.951
193.14964.71830.88377.06851.33260.477-0.13880.13230.26580.0270.1941-0.0491-0.14420.0174-0.05530.07950.02310.00620.0705-0.01780.083818.069954.51336.3234
205.57544.3415-0.16827.1669-0.18330.12360.03-0.15350.0253-0.0839-0.06230.21560.0907-0.00980.0323-0.00780.0098-0.00340.01990.0009-0.0222-2.909636.99856.4814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 18
2X-RAY DIFFRACTION2X19 - 29
3X-RAY DIFFRACTION3X30 - 38
4X-RAY DIFFRACTION4X39 - 52
5X-RAY DIFFRACTION5X53 - 66
6X-RAY DIFFRACTION6X67 - 86
7X-RAY DIFFRACTION7X87 - 92
8X-RAY DIFFRACTION8X93 - 110
9X-RAY DIFFRACTION9X111 - 154
10X-RAY DIFFRACTION10X155 - 163
11X-RAY DIFFRACTION11X164 - 188
12X-RAY DIFFRACTION12X189 - 201
13X-RAY DIFFRACTION13X202 - 216
14X-RAY DIFFRACTION14X217 - 230
15X-RAY DIFFRACTION15X231 - 240
16X-RAY DIFFRACTION16X241 - 249
17X-RAY DIFFRACTION17X250 - 257
18X-RAY DIFFRACTION18X258 - 264
19X-RAY DIFFRACTION19X265 - 277
20X-RAY DIFFRACTION20X278 - 283

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