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- PDB-2k4t: Solution structure of human VDAC-1 in LDAO micelles -

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Basic information

Entry
Database: PDB / ID: 2k4t
TitleSolution structure of human VDAC-1 in LDAO micelles
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsMEMBRANE 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 / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / neuron-neuron synaptic transmission / Mitochondrial calcium ion transport / regulation of autophagy of mitochondrion / calcium import into the mitochondrion / ceramide binding / mitochondrial permeability transition pore complex / voltage-gated monoatomic ion channel activity ...negative regulation of calcium import into the mitochondrion / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / neuron-neuron synaptic transmission / Mitochondrial calcium ion transport / regulation of autophagy of mitochondrion / calcium import into the mitochondrion / ceramide binding / mitochondrial permeability transition pore complex / voltage-gated monoatomic ion channel activity / Mitochondrial protein import / phosphatidylcholine binding / positive regulation of type 2 mitophagy / oxysterol binding / Pyruvate metabolism / monoatomic anion transport / pyruvate metabolic process / cholesterol binding / lipid transport / porin activity / pore complex / mitochondrial nucleoid / negative regulation of reactive oxygen species metabolic process / behavioral fear response / epithelial cell differentiation / learning / PINK1-PRKN Mediated Mitophagy / mitochondrial membrane / mitochondrial outer membrane / transmembrane transporter binding / Ub-specific processing proteases / positive regulation of apoptotic process / membrane raft / apoptotic process / synapse / negative regulation of apoptotic process / protein kinase binding / mitochondrion / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / 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
Non-selective voltage-gated ion channel VDAC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHiller, S. / Garces, R.G. / Malia, T.J. / Orekhov, V.Y. / Colombini, M. / Wagner, G.
CitationJournal: 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
DepositionJun 17, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)31,8791
Polymers31,8791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500target function
RepresentativeModel #1closest to the average

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Components

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


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 1H-15N NOESY, 3D 1H-13C NOESY, 4D NUS-MDD-1H-13C-13C NOESY, 4D NUS-MDD-1H-15N-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N; U-2H] VDAC-1, 93% H2O/7% D2O / Solvent system: 93% H2O/7% D2O
SampleConc.: 1 mM / Component: VDAC-1 / Isotopic labeling: [U-13C; U-15N; U-2H]
Sample conditionsIonic strength: 25 / pH: 7 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20

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