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- PDB-1okc: structure of mitochondrial ADP/ATP carrier in complex with carbox... -

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Basic information

Entry
Database: PDB / ID: 1okc
Titlestructure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside
ComponentsADP, ATP CARRIER PROTEIN HEART ISOFORM T1Adenosine diphosphate
KeywordsTRANSPORT PROTEIN / MITOCHONDRIAL TRANSPORTER / NUCLEOTIDE TRANSLOCATION / MEMBRANE PROTEIN / CARRIER PROTEIN
Function / homology
Function and homology information


ATP:ADP antiporter activity / ADP transport / mitochondrial ADP transmembrane transport / oxidative phosphorylation uncoupler activity / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / mitochondrial ATP transmembrane transport / Mitochondrial protein import / adaptive thermogenesis / positive regulation of mitophagy / mitochondrial permeability transition pore complex ...ATP:ADP antiporter activity / ADP transport / mitochondrial ADP transmembrane transport / oxidative phosphorylation uncoupler activity / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / mitochondrial ATP transmembrane transport / Mitochondrial protein import / adaptive thermogenesis / positive regulation of mitophagy / mitochondrial permeability transition pore complex / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of mitochondrial membrane permeability / mitochondrial membrane / mitochondrial inner membrane
Similarity search - Function
Mitochondrial carrier fold / Mitochondrial carrier domain / ADP/ATP carrier protein, eukaryotic type / Mitochondrial carrier protein / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
CARDIOLIPIN / Carboxyatractyloside / 3-LAURYLAMIDO-N,N'-DIMETHYLPROPYLAMINOXYDE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / ADP/ATP translocase 1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsPebay-Peyroula, E. / Dahout-Gonzalez, C. / Kahn, R. / Trezeguet, V. / Lauquin, G.J.-M. / Brandolin, G.
CitationJournal: Nature / Year: 2003
Title: Structure of Mitochondrial Adp/ATP Carrier in Complex with Carboxyatractyloside
Authors: Pebay-Peyroula, E. / Dahout-Gonzalez, C. / Kahn, R. / Trezeguet, V. / Lauquin, G.J.-M. / Brandolin, G.
History
DepositionJul 21, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Advisory / Derived calculations ...Advisory / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Remark 650 HELIX THE OVERALL STRUCTURE CONSISTS OF SIX TRANSMEMBRANE HELICES, MADE UP BY RESIDUES 3-38, 72- ... HELIX THE OVERALL STRUCTURE CONSISTS OF SIX TRANSMEMBRANE HELICES, MADE UP BY RESIDUES 3-38, 72-100, 107-143, 175-200, 208-239 AND 272-291. THERE ARE THREE HELICES ON THE MATRIX SIDE MADE UP BY RESIDUES 52-65, 155-168 AND 252-265.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP, ATP CARRIER PROTEIN HEART ISOFORM T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,80411
Polymers32,8791
Non-polymers8,92410
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.437, 83.463, 49.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 / Adenosine diphosphate / ADP/ATP TRANSLOCASE 1 / ADENINE NUCLEOTIDE TRANSLOCATOR 1 / ANT 1


Mass: 32879.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P02722

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Non-polymers , 5 types, 93 molecules

#2: Chemical ChemComp-CXT / Carboxyatractyloside / Carboxyatractyloside


Mass: 770.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H46O18S2
#3: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#4: Chemical ChemComp-LDM / 3-LAURYLAMIDO-N,N'-DIMETHYLPROPYLAMINOXYDE / [3-(DODECANOYLAMINO)PROPYL](HYDROXY)DIMETHYLAMMONIUM


Mass: 300.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H36N2O2
#5: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYZES THE EXCHANGE OF ADP AND ATP ACROSS THE MITOCHONDRIAL INNER MEMBRANE. MEMBER OF THE ...CATALYZES THE EXCHANGE OF ADP AND ATP ACROSS THE MITOCHONDRIAL INNER MEMBRANE. MEMBER OF THE MITOCHONDRIAL CARRIER FAMILY.

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Description: HEAVY ATOM DERIVATIVE DATA SETS WERE COLLECTED ON BEAMLINE BM30A AT ESRF
Crystal growpH: 8.5
Details: 30% JEFFAMINE600, 5MM NA CITRATE, 100MM TRIS PH 8.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
128-32 %Jeffamine-M6001reservoir
220 mM1reservoirNiSO4
3100 mMHEPES1reservoirpH7.0
410 mg/mlprotein1drop
55 mM1dropNaClor 100mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.72
DetectorDate: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 18544 / % possible obs: 99.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.4 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→14.99 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1354044.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 894 4.8 %RANDOM
Rwork0.22 ---
obs0.22 18544 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.7225 Å2 / ksol: 0.344655 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å20 Å2
2--1.24 Å20 Å2
3----4.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 349 83 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it9.952
X-RAY DIFFRACTIONc_scangle_it11.752.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 151 5 %
Rwork0.234 2885 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CAT-NEW4.PARCAT-NEW4.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
X-RAY DIFFRACTION5CDL-ENTIER.PARCDL-ENTIER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

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