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- PDB-7qi2: Magic-angle spinning NMR structure of the human voltage-dependent... -

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Basic information

Entry
Database: PDB / ID: 7qi2
TitleMagic-angle spinning NMR structure of the human voltage-dependent anion channel 1 (E73V/C127A/C232S) in DMPC lipid bilayers
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsMEMBRANE PROTEIN / solid-state NMR spectroscopy / magic-angle spinning / gating / voltage-dependent anion channel
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 domain superfamily
Similarity search - Domain/homology
Voltage-dependent anion-selective channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / na
AuthorsNajbauer, E.E. / Andreas, L.B.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 803 project A04 Germany
Max Planck Society Germany
German Research Foundation (DFG)Emmy Noether Program grant AN1316/1-1 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Structure and Gating Behavior of the Human Integral Membrane Protein VDAC1 in a Lipid Bilayer.
Authors: Najbauer, E.E. / Tekwani Movellan, K. / Giller, K. / Benz, R. / Becker, S. / Griesinger, C. / Andreas, L.B.
History
DepositionDec 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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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)31,8011
Polymers31,8011
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 2400target 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: 31800.553 Da / Num. of mol.: 1 / Mutation: E73V/C127A/C232S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VDAC1, VDAC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21796

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic1hCANH
121anisotropic1hcoCAcoNH
131anisotropic1hCONH
141anisotropic1hCOcaNH
151anisotropic2hcaCBcaNH
1101anisotropic2hcaCBcacoNH
191anisotropic1hNcacoNH
181anisotropic1hNcocaNH
171anisotropic1hCOCANH
161anisotropic1hcoCACONH
1131anisotropic1hCOCAnH
1121anisotropic1HNhhNH
1112anisotropic1hNCAH
1142anisotropic1hNcoCAH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid166 % w/w [U-13C; U-15N; U-2H] u[2H,13C,15N]-hVDAC1(E73V/C127A/C232S), 33 % w/w DMPC, 10 mM MES, 150 mM sodium chloride, 20 mM MgCl2, 100% H2ODMPC 2D crystals. The sample was 100% back-exchanged in H2Ou[2H,13C,15N]-hVDAC1(E73V/C127A/C232S)100% H2O
solid266 % w/w [U-13C; U-15N]-alpha PET u[2H,13C,15N]-hVDAC1(E73V/C127A/C232S), 33 % w/w DMPC, 10 mM MES, 150 mM sodium chloride, 20 mM MgCl2, 100% H2ODMPC 2D crystals. The sample was prepared with alpha-PET labeling, and the amide protons were100% back-exchanged in H2O.alpha-PET-hVDAC1(E73V/C127A/C232S)100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
66 % w/wu[2H,13C,15N]-hVDAC1(E73V/C127A/C232S)[U-13C; U-15N; U-2H]1
33 % w/wDMPCnatural abundance1
10 mMMESnatural abundance1
150 mMsodium chloridenatural abundance1
20 mMMgCl2natural abundance1
66 % w/wu[2H,13C,15N]-hVDAC1(E73V/C127A/C232S)[U-13C; U-15N]-alpha PET2
33 % w/wDMPCnatural abundance2
10 mMMESnatural abundance2
150 mMsodium chloridenatural abundance2
20 mMMgCl2natural abundance2
Sample conditionsIonic strength: 0.21 M / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD80011.3 mm probe, 55 kHz MAS
Bruker AVANCE III HDBrukerAVANCE III HD95020.7 mm probe, 90.909 kHz MAS

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3.98.13Guntert, Mumenthaler and Wuthrichchemical shift assignment
Sparky3.113Goddardpeak picking
Sparky3.113Goddardchemical shift assignment
TopSpin3.5pl7Bruker Biospincollection
TopSpin3.5pl7Bruker Biospinprocessing
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 2400 / Conformers submitted total number: 10

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