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- PDB-2c3e: The bovine mitochondrial ADP-ATP carrier -

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Basic information

Entry
Database: PDB / ID: 2c3e
TitleThe bovine mitochondrial ADP-ATP carrier
ComponentsADP/ATP TRANSLOCASE 1
KeywordsTRANSPORT PROTEIN / MITOCHONDRIAL CARRIER / NUCLEOTIDE TRANSPORT / MEMBRANE 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 / adaptive thermogenesis / Mitochondrial protein import / 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 / adaptive thermogenesis / Mitochondrial protein import / 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 / ADP/ATP translocase 1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNury, H. / Dahout-Gonzalez, C. / Trezeguet, V. / Lauquin, G. / Brandolin, G. / Pebay-Peyroula, E.
CitationJournal: FEBS Lett. / Year: 2005
Title: Structural Basis for Lipid-Mediated Interactions between Mitochondrial Adp/ATP Carrier Monomers.
Authors: Nury, H. / Dahout-Gonzalez, C. / Trezeguet, V. / Lauquin, G. / Brandolin, G. / Pebay-Peyroula, E.
History
DepositionOct 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP/ATP TRANSLOCASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0425
Polymers32,8791
Non-polymers5,1634
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.246, 110.752, 89.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ADP/ATP TRANSLOCASE 1 / ADENINE NUCLEOTIDE TRANSLOCATOR 1 / ANT 1 / ADP-ATP CARRIER PROTEIN 1 / SOLUTE CARRIER FAMILY 25 ...ADENINE NUCLEOTIDE TRANSLOCATOR 1 / ANT 1 / ADP-ATP CARRIER PROTEIN 1 / SOLUTE CARRIER FAMILY 25 MEMBER 4 / ADP / ATP CARRIER PROTEIN / HEART ISOFORM T1


Mass: 32879.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / References: UniProt: P02722
#2: Chemical ChemComp-CXT / 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


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
Compound detailsCATALYZES THE EXCHANGE OF ADP AND ATP ACROSS THE MITOCHONDRIAL INNER MEMBRANE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 53.82 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 9435 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 16.7 % / Biso Wilson estimate: 87 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OKC

1okc


Resolution: 2.8→25 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 459 4.8 %RANDOM
Rwork0.2497 ---
obs0.2497 9435 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.8507 Å2 / ksol: 0.32424 e/Å3
Displacement parametersBiso mean: 95.3 Å2
Baniso -1Baniso -2Baniso -3
1--33.319 Å20 Å20 Å2
2---0.002 Å20 Å2
3---33.321 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 249 0 2515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 80 0.054 %
Rwork0.313 1402 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CAT-NEW4.PARCAT-NEW4.PAR
X-RAY DIFFRACTION3CDL-ENTIER.PARCDL-ENTIER.TOP

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