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- PDB-4c9h: Structure of yeast mitochondrial ADP/ATP carrier isoform 2 inhibi... -

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Basic information

Entry
Database: PDB / ID: 4c9h
TitleStructure of yeast mitochondrial ADP/ATP carrier isoform 2 inhibited by carboxyatractyloside (P212121 crystal form)
ComponentsADP, ATP CARRIER PROTEIN 2
KeywordsTRANSPORT PROTEIN / MITOCHONDRIAL CARRIER / ADP/ATP CARRIER
Function / homology
Function and homology information


Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / ATP:ADP antiporter activity / ADP transport / mitochondrial ADP transmembrane transport / Mitochondrial protein import / mitochondrial ATP transmembrane transport / heme transport / ATP transport / anaerobic respiration / mitochondrial transport ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / ATP:ADP antiporter activity / ADP transport / mitochondrial ADP transmembrane transport / Mitochondrial protein import / mitochondrial ATP transmembrane transport / heme transport / ATP transport / anaerobic respiration / mitochondrial transport / aerobic respiration / transmembrane transport / mitochondrial inner membrane / apoptotic process / mitochondrion / 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 carrier protein 2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRuprecht, J.J. / Hellawell, A.M. / Harding, M. / Crichton, P.G. / McCoy, A.J. / Kunji, E.R.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structures of Yeast Mitochondrial Adp/ATP Carriers Support a Domain-Based Alternating-Access Transport Mechanism
Authors: Ruprecht, J.J. / Hellawell, A.M. / Harding, M. / Crichton, P.G. / Mccoy, A.J. / Kunji, E.R.S.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP, ATP CARRIER PROTEIN 2
B: ADP, ATP CARRIER PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,75711
Polymers68,9362
Non-polymers10,8209
Water00
1
A: ADP, ATP CARRIER PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1266
Polymers34,4681
Non-polymers5,6585
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP, ATP CARRIER PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6315
Polymers34,4681
Non-polymers5,1634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.354, 98.203, 105.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9944, -0.1053, 0.0018), (0.1054, -0.9944, 0.0046), (0.0013, 0.0048, 1)
Vector: -0.2554, -2.2356, -0.2921)

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Components

#1: Protein ADP, ATP CARRIER PROTEIN 2 / ADP/ATP TRANSLOCASE 2 / ADENINE NUCLEOTIDE TRANSLOCATOR 2 / ANT 2 / PETITE COLONIES PROTEIN 9 / ADP- ...ADP/ATP TRANSLOCASE 2 / ADENINE NUCLEOTIDE TRANSLOCATOR 2 / ANT 2 / PETITE COLONIES PROTEIN 9 / ADP-ATP CARRIER ISOFORM 2


Mass: 34468.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PYES3 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): WB12 / References: UniProt: P18239
#2: Chemical ChemComp-CXT / Carboxyatractyloside


Mass: 770.816 Da / Num. of mol.: 2 / 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.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#4: Chemical ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
Nonpolymer detailsCARDIOLIPIN (CDL): CARDIOLIPIN ACYL CHAINS ARE MODELLED IN PART

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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: 2.5 Å3/Da / Density % sol: 50.5 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS PH 8.5, 10MM SODIUM CITRATE, 50MM AMMONIUM SULFATE, 8% T-BUTANOL, 23.5% PEG600.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→19.84 Å / Num. obs: 11939 / % possible obs: 99.5 % / Observed criterion σ(I): 6 / Redundancy: 3.6 % / Biso Wilson estimate: 47.01 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.9
Reflection shellResolution: 3.2→3.46 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C9G

4c9g


Resolution: 3.2→19.839 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 567 4.8 %
Rwork0.2491 --
obs0.2506 11888 99.68 %
Refinement stepCycle: LAST / Resolution: 3.2→19.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 365 0 4475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034551
X-RAY DIFFRACTIONf_angle_d0.8266148
X-RAY DIFFRACTIONf_dihedral_angle_d17.4951725
X-RAY DIFFRACTIONf_chiral_restr0.042687
X-RAY DIFFRACTIONf_plane_restr0.002740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.52060.31611390.27792778X-RAY DIFFRACTION100
3.5206-4.02630.29381380.25852785X-RAY DIFFRACTION100
4.0263-5.05880.26571540.22832815X-RAY DIFFRACTION100
5.0588-19.83910.26461360.24622943X-RAY DIFFRACTION99

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