Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF YEAST MITOCHONDRIAL ADP/ATP CARRIER ISOFORM 2 INHIBITED BY CARBOXYATRACTYLOSIDE (C2221 CRYSTAL FORM)
 
Authors :  J. J. Ruprecht, A. M. Hellawell, M. Harding, P. G. Crichton, A. J. Mccoy, E. R. S. Kunji
Date :  02 Oct 13  (Deposition) - 22 Jan 14  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A
Keywords :  Mitochondrial Carrier, Adp/Atp Carrier, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. J. Ruprecht, A. M. Hellawell, M. Harding, P. G. Crichton, A. J. Mccoy E. R. S. Kunji
Structures Of Yeast Mitochondrial Adp/Atp Carriers Support A Domain-Based Alternating-Access Transport Mechanism
Proc. Natl. Acad. Sci. Usa V. 111 E426 2014
PubMed-ID: 24474793  |  Reference-DOI: 10.1073/PNAS.1320692111

(-) Compounds

Molecule 1 - ADP, ATP CARRIER PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System PlasmidPYES3
    Expression System StrainWB12
    Expression System Taxid4932
    Expression System Vector TypePLASMID
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymADP/ATP TRANSLOCASE 2, ADENINE NUCLEOTIDE TRANSLOCATOR 2, ANT 2, PETITE COLONIES PROTEIN 9, ADP-ATP CARRIER ISOFORM 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1BNG1Ligand/IonB-NONYLGLUCOSIDE
2CDL3Ligand/IonCARDIOLIPIN
3CXT1Ligand/IonCARBOXYATRACTYLOSIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:96 , ASN A:104 , LYS A:108 , GLY A:199 , ARG A:204 , SER A:245 , ASP A:249 , ARG A:252BINDING SITE FOR RESIDUE CXT A 401
2AC2SOFTWARETRP A:87 , ARG A:88 , GLY A:89 , ASN A:90 , THR A:91 , LEU A:173 , ILE A:174BINDING SITE FOR RESIDUE CDL A 800
3AC3SOFTWAREILE A:51 , GLY A:69 , ILE A:70 , LEU A:71 , PHE A:285 , LYS A:286 , GLY A:287 , CYS A:288 , GLY A:289 , ALA A:290 , ILE A:292 , LEU A:293BINDING SITE FOR RESIDUE CDL A 801
4AC4SOFTWARETYR A:190 , ARG A:191 , GLY A:192 , PHE A:193 , LEU A:194 , VAL A:198 , LEU A:248 , MET A:255 , GLY A:267 , ALA A:268 , PHE A:269BINDING SITE FOR RESIDUE CDL A 802
5AC5SOFTWAREASP A:55 , LEU A:58 , LYS A:59 , GLY A:61 , ASP A:212BINDING SITE FOR RESIDUE BNG A1310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C9G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C9G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C9G)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOLCARPS50920 Solute carrier (Solcar) repeat profile.ADT2_YEAST21-114
125-217
225-311
  2-
A:125-214
A:228-309

(-) Exons   (0, 0)

(no "Exon" information available for 4C9G)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:265
 aligned with ADT2_YEAST | P18239 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:286
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303      
           ADT2_YEAST    24 LIDFLMGGVSAAVAKTAASPIERVKLLIQNQDEMLKQGTLDRKYAGILDCFKRTATQEGVISFWRGNTANVIRYFPTQALNFAFKDKIKAMFGFKKEEGYAKWFAGNLASGGAAGALSLLFVYSLDYARTRLAADSKSSKKGGARQFNGLIDVYKKTLKSDGVAGLYRGFLPSVVGIVVYRGLYFGMYDSLKPLLLTGSLEGSFLASFLLGWVVTTGASTCSYPLDTVRRRMMMTSGQAVKYDGAFDCLRKIVAAEGVGSLFKGCGANILRGVAGAGVISMYDQLQ 309
               SCOP domains d4c9ga_ A: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--------....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh-------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SOLCAR  PDB: - UniProt: 21-114                                                             ----------SOLCAR  PDB: A:125-214 UniProt: 125-217                                                      -------SOLCAR  PDB: A:228-309 UniProt: 225-311                                               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c9g A  24 LIDFLMGGVSAAVAKTAASPIERVKLLIQNQDEMLKQGTLDRKYAGILDCFKRTATQEGVISFWRGNTANVIRYFPTQALNFAFKDKIKAMFGFKKEEGYAKWFAGNLASGGAAGALSLLFVYSLDYARTRLAADS--------RQFNGLIDVYKKTLKSDGVAGLYRGFLPSVVGIVVYRGLYFGMYDSL-------------LASFLLGWVVTTGASTCSYPLDTVRRRMMMTSGQAVKYDGAFDCLRKIVAAEGVGSLFKGCGANILRGVAGAGVISMYDQLQ 309
                                    33        43        53        63        73        83        93       103       113       123       133       143       153     |   -    |  173       183       193       203       213|        -    |  233       243       253       263       273       283       293       303      
                                                                                                                                                                 159      168                                           214           228                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C9G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C9G)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ADT2_YEAST | P18239)
molecular function
    GO:0005471    ATP:ADP antiporter activity    Catalysis of the reaction: ATP(out) + ADP(in) = ATP(in) + ADP(out).
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0015866    ADP transport    The directed movement of ADP, adenosine diphosphate, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015867    ATP transport    The directed movement of ATP, adenosine triphosphate, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0009060    aerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
    GO:0009061    anaerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0015886    heme transport    The directed movement of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006839    mitochondrial transport    Transport of substances into, out of or within a mitochondrion.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BNG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CDL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CXT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4c9g)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4c9g
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ADT2_YEAST | P18239
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ADT2_YEAST | P18239
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ADT2_YEAST | P182394c9h

(-) Related Entries Specified in the PDB File

4c9h STRUCTURE OF YEAST MITOCHONDRIAL ADP-ATP CARRIER ISOFORM 2 INHIBITED BY CARBOXYATRACTYLOSIDE (P212121 CRYSTAL FORM)
4c9j STRUCTURE OF YEAST MITOCHONDRIAL ADP-ATP CARRIER ISOFORM 3 INHIBITED BY CARBOXYATRACTYLOSIDE (P212121 CRYSTAL FORM)
4c9q STRUCTURE OF YEAST MITOCHONDRIAL ADP-ATP CARRIER ISOFORM 3 INHIBITED BY CARBOXYATRACTYLOSIDE (P21 CRYSTAL FORM)