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- PDB-6g73: The dynamic nature of the VDAC1 channels in bilayers: human VDAC1... -

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Basic information

Entry
Database: PDB / ID: 6g73
TitleThe dynamic nature of the VDAC1 channels in bilayers: human VDAC1 at 3.3 Angstrom resolution
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsTRANSPORT PROTEIN / ion-channel / B-barrel / outer mitochondrial membrane / cytochrome c release / APOPTOSIS
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
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Voltage-dependent anion-selective channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.27 Å
AuthorsRazeto, A. / Gribbon, P. / Loew, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other private Germany
CitationJournal: To Be Published
Title: The dynamic nature of the VDAC1 channels in bilayers as revealed by two crystal structures of the human isoform in bicelles at 2.7 and 3.3 Angstrom resolution: implications for VDAC1 voltage- ...Title: The dynamic nature of the VDAC1 channels in bilayers as revealed by two crystal structures of the human isoform in bicelles at 2.7 and 3.3 Angstrom resolution: implications for VDAC1 voltage-dependent mechanism and for its oligomerization
Authors: Razeto, A. / Gribbon, P. / Loew, C.
History
DepositionApr 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn / struct_conn_type / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Voltage-dependent anion-selective channel protein 1
B: Voltage-dependent anion-selective channel protein 1
C: Voltage-dependent anion-selective channel protein 1
D: Voltage-dependent anion-selective channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9049
Polymers127,5154
Non-polymers3,3905
Water0
1
C: Voltage-dependent anion-selective channel protein 1
D: Voltage-dependent anion-selective channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4353
Polymers63,7572
Non-polymers6781
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-32 kcal/mol
Surface area34040 Å2
MethodPISA
2
A: Voltage-dependent anion-selective channel protein 1
B: Voltage-dependent anion-selective channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4696
Polymers63,7572
Non-polymers2,7124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-37 kcal/mol
Surface area34130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.220, 83.360, 156.930
Angle α, β, γ (deg.)90.000, 90.590, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA2 - 2812 - 281
21PHEPHEBB2 - 2812 - 281
12PHEPHEAA2 - 2812 - 281
22PHEPHECC2 - 2812 - 281
13ALAALAAA2 - 2832 - 283
23ALAALADD2 - 2832 - 283
14GLNGLNBB2 - 2822 - 282
24GLNGLNCC2 - 2822 - 282
15PHEPHEBB2 - 2812 - 281
25PHEPHEDD2 - 2812 - 281
16PHEPHECC2 - 2812 - 281
26PHEPHEDD2 - 2812 - 281

NCS ensembles :
ID
1
2
3
4
5
6

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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.: 4
Source method: isolated from a genetically manipulated source
Details: C-terminal His6-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: VDAC1, VDAC / Plasmid: pET21a / Details (production host): C-term His6-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21796
#2: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.74 % / Description: Rods of dimensions 10x25x150 micrometers
Crystal growTemperature: 292.2 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25.5% Precipitant mix 4 [precipitant mix 4 consists of 25% (v/v) MPD, 25% (w/v) PEG1000, 25% (w/v) PEG3350], 0.06M NaNO3, 0.08M K2HPO4, 0.1M Buffer System2 [HEPES and MOPS adjusted to pH 7.5]

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 26, 2017
RadiationMonochromator: KB-mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.81
11h,-k,-l20.19
ReflectionResolution: 3.3→19.94 Å / Num. obs: 23523 / % possible obs: 99.5 % / Redundancy: 6.107 % / Biso Wilson estimate: 91.497 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.176 / Χ2: 0.924 / Net I/σ(I): 6.49 / Num. measured all: 143645 / Scaling rejects: 94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.66.0820.7741.9632577537853560.8390.84799.6
3.6-46.3810.483.3431177491648860.930.52299.4
4-4.55.9770.2126.2223347392139060.9860.23199.6
4.5-56.2940.1589.2315804252725110.990.17299.4
5-65.9940.1538.8917312289328880.9880.16799.8
6-106.0630.09511.9718790311530990.9970.10399.5
10-205.5280.06617.9442297797650.9980.07398.2
19.94-203.6520.05316.894091161120.9990.06396.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.92 Å48.81 Å
Translation6.92 Å48.81 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.6.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3emn

3emn


Resolution: 3.27→19.94 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.886 / SU B: 20.46 / SU ML: 0.351 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 1149 4.9 %RANDOM
Rwork0.2366 ---
obs0.2394 22261 96.21 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 267.42 Å2 / Biso mean: 108.801 Å2 / Biso min: 26.03 Å2
Baniso -1Baniso -2Baniso -3
1--61.54 Å20 Å2-11.61 Å2
2--123.66 Å20 Å2
3----62.12 Å2
Refinement stepCycle: final / Resolution: 3.27→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8640 0 115 0 8755
Biso mean--77.63 --
Num. residues----1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.028830
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.96411902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51551122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.02725.229371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.835151482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2911527
X-RAY DIFFRACTIONr_chiral_restr0.1010.21317
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026568
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A145480.13
12B145480.13
21A148700.12
22C148700.12
31A149000.12
32D149000.12
41B152000.11
42C152000.11
51B150620.12
52D150620.12
61C142300.11
62D142300.11
LS refinement shellResolution: 3.269→3.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 62 -
Rwork0.397 1046 -
all-1108 -
obs--60.98 %

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