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- PDB-6tiq: Refined solution NMR structure of hVDAC-1 in detergent micelles -

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Basic information

Entry
Database: PDB / ID: 6tiq
TitleRefined solution NMR structure of hVDAC-1 in detergent micelles
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsTRANSPORT PROTEIN / beta-barrel membrane protein VDAC pore
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
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
Voltage-dependent anion-selective channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBoehm, R. / Hiller, S. / Wagner, G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research Council281764 Switzerland
CitationJournal: Structure / Year: 2020
Title: The Structural Basis for Low Conductance in the Membrane Protein VDAC upon beta-NADH Binding and Voltage Gating.
Authors: Bohm, R. / Amodeo, G.F. / Murlidaran, S. / Chavali, S. / Wagner, G. / Winterhalter, M. / Brannigan, G. / Hiller, S.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)31,8791
Polymers31,8791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17400 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Voltage-dependent anion-selective channel protein 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P21796

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D 1H-15N NOESY
123isotropic13D 1H-13C NOESY
132isotropic14D NUS-MDD-1H-13C-13C
143isotropic14D NUS-MDD-1H-15N-13C
151isotropic13D HNCO
161isotropic13D HNCA
171isotropic13D HN(CA)CB
181isotropic13D HN(CO)CA

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle10.6 mM U-99%-2H,13C,15N hVDAC-1, 3 % no LDAO, 95% H2O/5% D2O15N_13C_sample95% H2O/5% D2O
micelle20.6 mM [ U -99%- 2 H, 13 C, 15 N; 99%- 1 H delta -IL; 99%- 1 H gamma -V] hVDAC-1, 3 % [U-99% 2H] LDAO, 95% H2O/5% D2O15N NOESY95% H2O/5% D2O
micelle30.6 mM [ U -99%- 2 H, 15 N; 99%- 1 H delta , 13 C delta -IL; 99%- 1 H gamma , 13 C gamma -V] hVDAC-1, 3 % [U-99% 2H] LDAO, 95% H2O/5% D2O13C NOESY95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMhVDAC-1U-99%-2H,13C,15N1
3 %LDAOno1
0.6 mMhVDAC-1[ U -99%- 2 H, 13 C, 15 N; 99%- 1 H delta -IL; 99%- 1 H gamma -V]2
3 %LDAO[U-99% 2H]2
0.6 mMhVDAC-1[ U -99%- 2 H, 15 N; 99%- 1 H delta , 13 C delta -IL; 99%- 1 H gamma , 13 C gamma -V]3
3 %LDAO[U-99% 2H]3
Sample conditionsIonic strength: 225 mM / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 303.15 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
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
XEASYBartels et al.peak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000 / Conformers submitted total number: 20

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