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- PDB-5xdo: Crystal structure of human voltage-dependent anion channel 1 (hVD... -

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Basic information

Entry
Database: PDB / ID: 5xdo
TitleCrystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsMEMBRANE PROTEIN / CELL-FREE SYNTHESIS / beta-barrel structure
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 / pyruvate metabolic process / oxysterol binding / monoatomic anion transport / cholesterol binding / porin activity / mitochondrial nucleoid / pore complex / 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 / synapse / apoptotic process / 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
HEXANE / PENTANE / N-OCTANE / SPERMIDINE / Voltage-dependent anion-selective channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHosaka, T. / Kimura-Someya, T. / Shirouzu, M.
CitationJournal: Protein Sci. / Year: 2017
Title: Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1
Authors: Hosaka, T. / Okazaki, M. / Kimura-Someya, T. / Ishizuka-Katsura, Y. / Ito, K. / Yokoyama, S. / Dodo, K. / Sodeoka, M. / Shirouzu, M.
History
DepositionMar 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)65,40411
Polymers64,4262
Non-polymers9789
Water32418
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint43 kcal/mol
Surface area32340 Å2
Unit cell
Length a, b, c (Å)121.620, 146.330, 77.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32213.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VDAC1, VDAC / Production host: Escherichia coli (E. coli) / References: UniProt: P21796

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Non-polymers , 5 types, 27 molecules

#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical
ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical ChemComp-LNK / PENTANE / Pentane


Mass: 72.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12
#5: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 45% PEG300, 0.1 M HEPES (pH 7.0), 0.15 M NaCl, 11 mM spermidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→47.848 Å / Num. obs: 24183 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.377 % / Biso Wilson estimate: 101.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.198 / Rrim(I) all: 0.209 / Χ2: 1 / Net I/σ(I): 10.26 / Num. measured all: 134064 / Scaling rejects: 33
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
3.1-3.189.6582.7070.990219359340.3012.86399.9
3.18-3.2710.811.781.5299249189180.6151.868100
3.27-3.3610.6541.3271.9794938918910.7861.393100
3.36-3.4710.4470.912.9588908518510.8690.957100
3.47-3.5810.5880.6583.8590008508500.9310.691100
3.58-3.7110.4520.5015.2886338278260.970.52699.9
3.71-3.8510.8110.4276.4583147697690.9630.448100
3.85-410.7150.3587.1781227587580.9740.376100
4-4.1810.6540.2619.7478417367360.9880.274100
4.18-4.3810.4450.1813.4873437037030.9920.189100
4.38-4.6210.0970.13816.3866646606600.9960.145100
4.62-4.910.2340.12916.8966016456450.9970.136100
4.9-5.2410.580.15715.3262005865860.9940.165100
5.24-5.6610.560.16214.7359245615610.9940.17100
5.66-6.210.3910.13316.7453415145140.9960.14100
6.2-6.9310.0480.11318.547834764760.9960.12100
6.93-810.0290.08322.0641824174170.9990.088100
8-9.810.0520.06826.9136993683680.9990.072100
9.8-13.869.4740.05231.4227002862850.9990.05599.7
13.86-47.8488.1230.03340.36138917817110.03696.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EMN

3emn


Resolution: 3.1→47.848 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2984 1206 4.99 %
Rwork0.2552 22977 -
obs0.2575 24183 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.14 Å2 / Biso mean: 103.7495 Å2 / Biso min: 30.28 Å2
Refinement stepCycle: final / Resolution: 3.1→47.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3965 0 68 18 4051
Biso mean--65.33 53.04 -
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014093
X-RAY DIFFRACTIONf_angle_d0.4415522
X-RAY DIFFRACTIONf_chiral_restr0.039633
X-RAY DIFFRACTIONf_plane_restr0.003703
X-RAY DIFFRACTIONf_dihedral_angle_d5.6922372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1001-3.22420.4441330.40282516264998
3.2242-3.37090.36911340.346425542688100
3.3709-3.54850.37811360.294725422678100
3.5485-3.77080.29631360.255225582694100
3.7708-4.06180.40861340.254425742708100
4.0618-4.47030.29221330.230125672700100
4.4703-5.11650.24591380.207325552693100
5.1165-6.44380.29691340.270325662700100
6.4438-47.85360.25061280.25242545267399
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)
13.4406-2.81060.81518.1324-0.44580.0818-0.48010.58910.91560.33950.4861-1.7654-0.46460.1458-0.00780.8193-0.0841-0.11750.907-0.01211.01-27.0381-4.370221.5504
27.68974.9311-2.64897.3844-5.8236.33290.37-0.89570.69060.2448-0.4308-0.404-0.0391.48170.04410.55850.1364-0.11050.9341-0.03240.9882-39.76627.451318.8477
31.2752-0.39220.91471.4995-0.59251.65310.1645-0.2154-0.2093-0.0791-0.04730.18390.09520.2115-0.15010.52630.0020.08220.7171-0.00590.8093-39.8269-16.732917.4422
44.5802-2.5985-2.96714.62880.93382.01430.345-0.0321-1.4716-0.1042-0.12830.11681.3702-0.5494-0.45890.9379-0.1919-0.12130.76590.02340.7813-72.1632-40.81720.0373
51.9204-3.68281.95757.6084-5.73418.19340.42450.5259-1.5427-1.65351.0576-0.09981.1366-0.4554-1.52330.9753-0.4371-0.41571.13380.48561.7303-76.4383-57.947924.7106
62.90842.67321.69972.58252.27114.649-0.24920.1453-1.4881-0.10270.89360.143-0.3395-0.126-0.41250.9132-0.28460.02640.80520.33831.2446-69.4425-60.015720.9225
74.49161.2383-4.97168.29061.27536.77060.6423-1.5939-2.1719-1.81950.76710.12740.55030.0425-1.20631.1392-0.0762-0.26250.8426-0.01891.5952-59.8203-59.506321.7458
82.3109-3.6610.4776.3969-2.28643.8428-0.0792-0.2115-0.2523-0.34520.00060.3227-0.01150.34120.05840.4748-0.0621-0.13220.80880.04490.8235-53.7533-41.020118.3688
98.07480.6232.3323.4522-1.89948.0997-0.0358-0.3853-0.4856-0.0498-0.20290.380.6682-0.93690.22990.7331-0.0482-0.01760.5093-0.02060.844-74.7308-27.987717.9664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 80 )A1 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 146 )A81 - 146
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 283 )A147 - 283
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 52 )B1 - 52
5X-RAY DIFFRACTION5chain 'B' and (resid 53 through 75 )B53 - 75
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 94 )B76 - 94
7X-RAY DIFFRACTION7chain 'B' and (resid 95 through 120 )B95 - 120
8X-RAY DIFFRACTION8chain 'B' and (resid 121 through 211 )B121 - 211
9X-RAY DIFFRACTION9chain 'B' and (resid 212 through 281 )B212 - 281

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