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- PDB-4c69: ATP binding to murine voltage-dependent anion channel 1 (mVDAC1). -

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Basic information

Entry
Database: PDB / ID: 4c69
TitleATP binding to murine voltage-dependent anion channel 1 (mVDAC1).
ComponentsVOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1
KeywordsTRANSPORT PROTEIN / BICELLE / OUTER MEMBRANE PROTEIN
Function / homology
Function and homology information


Pyruvate metabolism / 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 / PINK1-PRKN Mediated Mitophagy / neuron-neuron synaptic transmission / mitochondrial calcium ion transmembrane transport / acetyl-CoA biosynthetic process from pyruvate / ceramide binding / monoatomic anion channel activity ...Pyruvate metabolism / 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 / PINK1-PRKN Mediated Mitophagy / neuron-neuron synaptic transmission / mitochondrial calcium ion transmembrane transport / acetyl-CoA biosynthetic process from pyruvate / ceramide binding / monoatomic anion channel activity / regulation of mitophagy / mitochondrial permeability transition pore complex / phosphatidylcholine binding / Ub-specific processing proteases / oxysterol binding / cholesterol binding / porin activity / mitochondrial nucleoid / negative regulation of reactive oxygen species metabolic process / behavioral fear response / presynaptic active zone membrane / epithelial cell differentiation / learning / postsynaptic density membrane / synaptic vesicle / myelin sheath / chemical synaptic transmission / mitochondrial outer membrane / transmembrane transporter binding / mitochondrial inner membrane / membrane raft / nucleotide binding / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / membrane / identical protein binding / 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
ADENOSINE-5'-TRIPHOSPHATE / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Voltage-dependent anion-selective channel protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.277 Å
AuthorsPaz, A. / Colletier, J.P. / Abramson, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structure-Guided Simulations Illuminate the Mechanism of ATP Transport Through Vdac1.
Authors: Choudhary, O.P. / Paz, A. / Adelman, J.L. / Colletier, J. / Abramson, J. / Grabe, M.
History
DepositionSep 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Jul 16, 2014Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 19-STRANDED BARREL THIS IS REPRESENTED BY A 20-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,43510
Polymers32,1961
Non-polymers3,2399
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.152, 58.369, 66.545
Angle α, β, γ (deg.)90.00, 99.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1 / VDAC-1 / MVDAC1 / OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN 1 / PLASMALEMMAL PORIN / VOLTAGE- ...VDAC-1 / MVDAC1 / OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN 1 / PLASMALEMMAL PORIN / VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 5 / VDAC-5 / MVDAC5


Mass: 32195.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q60932
#2: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.87 % / Description: NONE
Crystal growpH: 8.5 / Details: 18-20% MPD, 0.1 M TRISHCL (PH 8.5), 10% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 16915 / % possible obs: 99.3 % / Observed criterion σ(I): 2.21 / Redundancy: 3.64 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.13
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.21 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EMN

3emn


Resolution: 2.277→19.497 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 30.02 / Stereochemistry target values: ML
Details: THE ATP MOLECULE WAS DOCKED BASED ON DENSITES GENERATED BY A FO-FO MAP OF THE DIFFERENCE BETWEEN THE ATP SOAKED DATASET AND A NATIVE ONE. THE FINAL HIGH B-FACTORS FOR THE REFINED ATP ...Details: THE ATP MOLECULE WAS DOCKED BASED ON DENSITES GENERATED BY A FO-FO MAP OF THE DIFFERENCE BETWEEN THE ATP SOAKED DATASET AND A NATIVE ONE. THE FINAL HIGH B-FACTORS FOR THE REFINED ATP STRONGLY SUGGEST THAT THE BINDING SITE IS A LOW-AFFINITY ONE IN WHICH ATP VIBRATES CONSIDERABLY AROUND ITS EQUILIBRIUM POSITION. THE COORDINATES REPRESENT THE MOST PROBABLE LOCATION OF THE ATP.
RfactorNum. reflection% reflection
Rfree0.2611 863 5 %
Rwork0.2037 --
obs0.2066 17142 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.277→19.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 143 54 2368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072396
X-RAY DIFFRACTIONf_angle_d1.1093241
X-RAY DIFFRACTIONf_dihedral_angle_d17.647919
X-RAY DIFFRACTIONf_chiral_restr0.077342
X-RAY DIFFRACTIONf_plane_restr0.004397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2773-2.41970.33851430.28432478X-RAY DIFFRACTION91
2.4197-2.60620.33331410.26892732X-RAY DIFFRACTION100
2.6062-2.86770.30791530.22852745X-RAY DIFFRACTION100
2.8677-3.2810.25231280.20972785X-RAY DIFFRACTION100
3.281-4.12720.2551530.19142744X-RAY DIFFRACTION99
4.1272-19.49720.24181450.18962795X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4061-0.24520.18085.4804-5.31067.6273-0.06070.0267-0.0521-0.37060.47210.62040.5731-0.3032-0.48960.3154-0.01090.04030.34120.02580.365511.762734.578622.4671
29.77784.3368-0.20844.2960.35892.73650.825-1.0044-0.17041.1055-0.66030.17260.42460.8523-0.25370.74620.07720.10340.92860.00540.480.961430.77015.9695
36.05336.5841-1.72429.1497-4.75848.0015-0.20490.5035-0.3574-0.2760.4004-0.717-0.6684-0.17790.01620.6360.1480.12550.9072-0.06240.63366.575427.68063.5657
44.7795-0.2899-1.069410.2138-2.1454.29940.4110.8085-0.5104-0.57150.03190.3066-0.0669-0.3671-0.19860.37880.1108-0.13350.7764-0.02760.43985.232117.30538.1724
58.81940.7704-5.65184.7612-2.67384.20330.32981.0092-0.1719-0.4208-0.1468-0.1012-0.1868-1.5288-0.23220.4821-0.0148-0.02670.6437-0.0640.33017.712612.698118.3581
63.94960.35060.59094.9488-2.38524.14720.35361.62590.5904-0.7480.2217-0.35510.00280.1364-0.30170.48320.1374-0.06330.92290.0120.521115.367915.565212.6682
77.5201-1.9626-0.42515.93084.99925.1960.08250.8241-0.5295-0.5404-0.05050.2052-0.4832-0.1162-0.38580.46560.0265-0.00360.30490.05890.300118.462817.449724.459
86.4576-1.8462-1.50257.06750.00674.2361-0.23910.1742-0.54850.14110.2557-0.31980.210.9167-0.25280.417-0.0261-0.06720.4931-0.03930.38924.108423.429127.3603
97.8626-6.03820.8348.2987-0.61984.8738-0.1486-0.1051-0.29280.1090.32980.1701-0.2769-0.2037-0.16630.4871-0.0287-0.04960.2827-0.01760.329316.912437.591429.9222
102.8208-0.00382.62983.1349-0.96062.511-0.27390.1296-0.2791-0.07830.23680.034-0.2225-0.17970.0360.57360.02420.09730.3775-0.06580.340817.947744.852425.0357
113.39962.36174.37744.95792.23935.6124-0.67960.2029-0.2022-0.65020.08060.3942-0.4235-0.69760.50080.62440.09440.08950.41940.01290.30547.972649.158518.1068
128.57630.62636.84333.16373.75019.0689-0.4380.63060.8814-0.09890.08850.2943-0.7789-0.10030.25910.64120.02420.01890.39410.1080.35676.121848.548610.0813
134.07842.41332.9584.53122.08975.62070.01431.37640.7105-0.06340.63910.3904-1.25230.4812-0.63860.96810.00240.09060.9233-0.0180.57318.431546.66485.7004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN X AND (RESID 1 THROUGH 25 )
2X-RAY DIFFRACTION2CHAIN X AND (RESID 26 THROUGH 48 )
3X-RAY DIFFRACTION3CHAIN X AND (RESID 49 THROUGH 64 )
4X-RAY DIFFRACTION4CHAIN X AND (RESID 65 THROUGH 88 )
5X-RAY DIFFRACTION5CHAIN X AND (RESID 89 THROUGH 103 )
6X-RAY DIFFRACTION6CHAIN X AND (RESID 104 THROUGH 120 )
7X-RAY DIFFRACTION7CHAIN X AND (RESID 121 THROUGH 146 )
8X-RAY DIFFRACTION8CHAIN X AND (RESID 147 THROUGH 174 )
9X-RAY DIFFRACTION9CHAIN X AND (RESID 175 THROUGH 199 )
10X-RAY DIFFRACTION10CHAIN X AND (RESID 200 THROUGH 225 )
11X-RAY DIFFRACTION11CHAIN X AND (RESID 226 THROUGH 241 )
12X-RAY DIFFRACTION12CHAIN X AND (RESID 242 THROUGH 267 )
13X-RAY DIFFRACTION13CHAIN X AND (RESID 268 THROUGH 283 )

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