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- PDB-5jdp: E73V mutant of the human voltage-dependent anion channel -

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Basic information

Entry
Database: PDB / ID: 5jdp
TitleE73V mutant of the human voltage-dependent anion channel
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsMEMBRANE PROTEIN / Structure refinement / Sparse data / Protein dynamics / Relaxation
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
AuthorsJaremko, M. / Jaremko, L. / Villinger, S. / Schmidt, C. / Giller, K. / Griesinger, C. / Becker, S. / Zweckstetter, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council282008 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: High-Resolution NMR Determination of the Dynamic Structure of Membrane Proteins.
Authors: Jaremko, M. / Villinger, S. / Schmidt, C.D. / Griesinger, C. / Becker, S. / Zweckstetter, M.
History
DepositionApr 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_sample_details.contents / _pdbx_nmr_spectrometer.model

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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)30,9781
Polymers30,9781
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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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: 30977.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: SAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTVKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQARS
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
111isotropic1R1 relaxation rate
121isotropic1R2 relaxation rate
131isotropic2R1 relaxation rate
141isotropic2R2 relaxation rate
151isotropic3R1 relaxation rate
161isotropic3R2 relaxation rate
171isotropic43D 1H-15N NOESY

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Sample preparation

DetailsType: micelle
Contents: 0.8 mM U- 2H, 15N_sample E73V mutant of the Voltage-dependent anion channel 1, 2 % [U-2H] LDAO, 20 mM [U-2H] TRIS, 90% H2O/10% D2O
Details: For the current 15N relaxation studies the E73V variant of human VDAC1 was prepared in U- 2H, 15N-labelled form and solubilized in 2% LDAO micelles.
Label: U- 2H, 15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mME73V mutant of the Voltage-dependent anion channel 1U- 2H, 15N_sample1
2 %LDAO[U-2H]1
20 mMTRIS[U-2H]1
Sample conditionsDetails: For the current 15N relaxation studies the E73V variant of human VDAC1 was prepared in U- 2H, 15N-labelled form and solubilized in 2% LDAO micelles.
Ionic strength: 20 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE9003
Bruker AVANCEBrukerAVANCE8004

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr AnalysisCCPNchemical shift assignment
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNpeak picking
NMR ensembleConformers submitted total number: 20

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