+Open data
-Basic information
Entry | Database: PDB / ID: 2k4t | ||||||
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Title | Solution structure of human VDAC-1 in LDAO micelles | ||||||
Components | Voltage-dependent anion-selective channel protein 1 | ||||||
Keywords | MEMBRANE PROTEIN / APOPTOSIS / Acetylation / Host-virus interaction / Ion transport / Membrane / Mitochondrion / Outer membrane / Phosphoprotein / Porin / Transmembrane / Transport Protein | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Hiller, S. / Garces, R.G. / Malia, T.J. / Orekhov, V.Y. / Colombini, M. / Wagner, G. | ||||||
Citation | Journal: Science / Year: 2008 Title: Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Authors: Hiller, S. / Garces, R.G. / Malia, T.J. / Orekhov, V.Y. / Colombini, M. / Wagner, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k4t.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2k4t.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 2k4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/2k4t ftp://data.pdbj.org/pub/pdb/validation_reports/k4/2k4t | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 31878.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VDAC1, VDAC / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21796 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 1H-15N NOESY, 3D 1H-13C NOESY, 4D NUS-MDD-1H-13C-13C NOESY, 4D NUS-MDD-1H-15N-13C NOESY |
-Sample preparation
Details | Contents: 1 mM [U-13C; U-15N; U-2H] VDAC-1, 93% H2O/7% D2O / Solvent system: 93% H2O/7% D2O |
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Sample | Conc.: 1 mM / Component: VDAC-1 / Isotopic labeling: [U-13C; U-15N; U-2H] |
Sample conditions | Ionic strength: 25 / pH: 7.0 / Pressure: AMBIENT / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20 |