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- PDB-2jk4: Structure of the human voltage-dependent anion channel -

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Basic information

Entry
Database: PDB / ID: 2jk4
TitleStructure of the human voltage-dependent anion channel
ComponentsVOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1
KeywordsTRANSPORT / VDAC / PORIN / MEMBRANE / APOPTOSIS / MITOCHONDRION OUTER MEMBRANE / MITOCHONDRIAL OUTER MEMBRANE / MEMBRANE PROTEIN / HOST-VIRUS INTERACTION / ION TRANSPORT / TRANSMEMBRANE / PHOSPHOPROTEIN / ACETYLATION / MITOCHONDRION / CELL MEMBRANE
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 domain superfamily
Similarity search - Domain/homology
Voltage-dependent anion-selective channel protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 4.1 Å
AuthorsBayrhuber, M. / Meins, T. / Habeck, M. / Becker, S. / Giller, K. / Villinger, S. / Vonrhein, C. / Griesinger, C. / Zweckstetter, M. / Zeth, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of the Human Voltage-Dependent Anion Channel.
Authors: Bayrhuber, M. / Meins, T. / Habeck, M. / Becker, S. / Giller, K. / Villinger, S. / Vonrhein, C. / Griesinger, C. / Zweckstetter, M. / Zeth, K.
History
DepositionAug 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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


Theoretical massNumber of molelcules
Total (without water)32,1821
Polymers32,1821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.990, 77.990, 167.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1 / VOLTAGE-DEPENDENT ANION CHANNEL ISOFORM 1 / VDAC-1 / HVDAC1 / OUTER MITOCHONDRIAL MEMBRANE PROTEIN ...VOLTAGE-DEPENDENT ANION CHANNEL ISOFORM 1 / VDAC-1 / HVDAC1 / OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN 1 / PLASMALEMMAL PORIN / PORIN 31HL / PORIN 31HM / HUMAN VDAC


Mass: 32181.988 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21796

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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: 4.5 Å3/Da / Density % sol: 73 % / Description: NONE
Crystal growDetails: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M HEPES SODIUM PH 7.5, 30% V/V POLYETHYLENE GLYCOL 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 4.1→43 Å / Num. obs: 4887 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 16.8 % / Biso Wilson estimate: 175.334 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.4
Reflection shellResolution: 4.1→4.3 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER-TNTrefinement
XDSdata reduction
SCALAdata scaling
SHELXDSOLOMON SHARPphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 4.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.3873 477 10 %RANDOM
Rwork0.325 ---
obs0.3314 4840 99.5 %-
Displacement parametersBiso mean: 179.12 Å2
Baniso -1Baniso -2Baniso -3
1--8.60559481 Å20 Å20 Å2
2---8.60559481 Å20 Å2
3---17.21118962 Å2
Refinement stepCycle: LAST / Resolution: 4.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 0 0 2207
LS refinement shellResolution: 4.1→4.35 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.232 81 11.76 %
Rwork0.2223 608 -
all0.2235 689 -
obs--97.98 %

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