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

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Basic information

Entry
Database: PDB / ID: 5xdn
TitleCrystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsMEMBRANE PROTEIN / beta-barrel structure / CELL-FREE SYNTHESIS
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
DECANE / DODECANE / HEXANE / N-OCTANE / Voltage-dependent anion-selective channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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

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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)65,51011
Polymers64,4262
Non-polymers1,0849
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint35 kcal/mol
Surface area32130 Å2
Unit cell
Length a, b, c (Å)58.700, 84.960, 146.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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, 65 molecules

#2: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26
#3: Chemical
ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 36% PEG300, 0.1 M MES (pH 6.5), 0.1 M NaCl

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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: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→45.86 Å / Num. obs: 12096 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 10.167 % / Biso Wilson estimate: 57.331 Å2 / CC1/2: 0.946 / Rmerge(I) obs: 0.385 / Rrim(I) all: 0.406 / Χ2: 0.69 / Net I/σ(I): 4.4 / Num. measured all: 122979 / Scaling rejects: 8
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
3.15-3.2310.5921.3691.41101269619560.7391.43899.5
3.23-3.3210.6491.1231.797449349150.821.17998
3.32-3.429.7490.9131.985609048780.910.96397.1
3.42-3.527.7850.6722.0533638844320.9430.71448.9
3.52-3.6410.3350.632.8486718548390.9310.66298.2
3.64-3.777.3310.692.1534608294720.9170.73656.9
3.77-3.9110.5710.5633.484258207970.9340.59297.2
3.91-4.0710.5140.5023.8778337677450.9470.52797.1
4.07-4.2510.6230.375.0677027477250.9770.38897.1
4.25-4.4510.4340.3266.0774297307120.980.34297.5
4.45-4.710.4410.2916.7568916806600.9860.30597.1
4.7-4.9810.5060.2826.6765986516280.990.29596.5
4.98-5.3210.560.3155.8862416135910.9710.33196.4
5.32-5.7510.4550.3095.8157715705520.980.32496.8
5.75-6.310.3940.296.0652805265080.9730.30596.6
6.3-7.0410.4090.276.3248094884620.9880.28494.7
7.04-8.1310.2880.286.7743624424240.9920.29595.9
8.13-9.9610.1470.287.835823743530.9640.29594.4
9.96-14.099.7330.3218.4327353022810.9170.34193
14.09-45.868.4160.288.7913971931660.9640.30186

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EMN

3emn


Resolution: 3.15→45.86 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.835 / SU B: 27.807 / SU ML: 0.469 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.605 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2998 564 4.7 %RANDOM
Rwork0.2658 ---
obs0.2673 11508 91.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.52 Å2 / Biso mean: 66.266 Å2 / Biso min: 13.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--3.75 Å2-0 Å2
3----3.47 Å2
Refinement stepCycle: final / Resolution: 3.15→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4167 0 76 56 4299
Biso mean--56.97 39.36 -
Num. residues----549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024319
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.9615795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7835542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10924.831178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95715712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8411514
X-RAY DIFFRACTIONr_chiral_restr0.0460.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023164
LS refinement shellResolution: 3.15→3.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 47 -
Rwork0.378 906 -
all-953 -
obs--99.37 %

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