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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YEAST INTER-MEMBRANE SPACE CHAPERONE ASSEMBLY TIM9.10
 
Authors :  C. T. Webb, J. M. Gulbis
Date :  24 Jul 08  (Deposition) - 23 Dec 08  (Release) - 17 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  A,B  (6x)
Keywords :  Alpha-Propeller; Helix-Turn-Helix; Intramolecular Disulfides. , Chaperone, Inner Membrane, Membrane, Metal- Binding, Mitochondrion, Protein Transport, Translocation, Transport, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Baker, C. T. Webb, D. A. Stroud, C. S. Palmer, A. E. Frazier, B. Guiard, A. Chacinska, J. M. Gulbis, M. T. Ryan
Structural And Functional Requirements For Activity Of The Tim9-Tim10 Complex In Mitochondrial Protein Import
Mol Biol Cell V. 20 769 2009
PubMed-ID: 19037098  |  Reference-DOI: 10.1091/MBC.E08-09-0903
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM9
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T2
    Expression System StrainORIGAMI DE3 PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTIM9
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
 
Molecule 2 - MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T2
    Expression System StrainORIGAMI DE3 PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMRS11, TIM10
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymMITOCHONDRIAL INTERMEMBRANE PROTEIN MRS11

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB
Biological Unit 2 (6x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3DXR)

(-) Sites  (0, 0)

(no "Site" information available for 3DXR)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:35 -A:59
2A:39 -A:55
3B:40 -B:65
4B:44 -B:61

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DXR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DXR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DXR)

(-) Exons   (0, 0)

(no "Exon" information available for 3DXR)

(-) Sequences/Alignments

Asymmetric 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:69
 aligned with TIM9_YEAST | O74700 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:69
                                    21        31        41        51        61        71         
            TIM9_YEAST   12 FQKVVEQKQMKDFMRLYSNLVERCFTDCVNDFTTSKLTNKEQTCIMKCSEKFLKHSERVGQRFQEQNAA 80
               SCOP domains d3dxra_ A: automated matches                                          SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  3dxr A 12 FQKVVEQKQMKDFMRLYSNLVERCFTDCVNDFTTSKLTNKEQTCIMKCSEKFLKHSERVGQRFQEQNAA 80
                                    21        31        41        51        61        71         

Chain B from PDB  Type:PROTEIN  Length:69
 aligned with TIM10_YEAST | P87108 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:69
                                    24        34        44        54        64        74         
           TIM10_YEAST   15 SQQKIQAAEAELDLVTDMFNKLVNNCYKKCINTSYSEGELNKNESSCLDRCVAKYFETNVQVGENMQKM 83
               SCOP domains d3dxrb_ B: automated matches                                          SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  3dxr B 15 SQQKIQAAEAELDLVTDMFNKLVNNCYKKCINTSYSEGELNKNESSCLDRCVAKYFETNVQVGENMQKM 83
                                    24        34        44        54        64        74         

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DXR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DXR)

(-) Gene Ontology  (15, 28)

Asymmetric Unit(hide GO term definitions)
Chain A   (TIM9_YEAST | O74700)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0072321    chaperone-mediated protein transport    The directed movement of proteins into, out of or within a cell, or between cells, mediated by chaperone molecules that bind to the transported proteins.
    GO:0045039    protein import into mitochondrial inner membrane    The process comprising the import of proteins into the mitochondrion from outside the organelle and their insertion into the mitochondrial inner membrane. The translocase of the outer membrane complex mediates the passage of these proteins across the outer membrane, after which they are guided by either of two inner membrane translocase complexes into their final destination in the inner membrane.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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: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:0042721    mitochondrial inner membrane protein insertion complex    A multi-subunit complex embedded in the mitochondrial inner membrane that mediates insertion of carrier proteins into the inner membrane.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0042719    mitochondrial intermembrane space protein transporter complex    Soluble complex of the mitochondrial intermembrane space composed of various combinations of small Tim proteins; acts as a protein transporter to guide proteins to the Tim22 complex for insertion into the mitochondrial inner membrane.
    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.

Chain B   (TIM10_YEAST | P87108)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0045039    protein import into mitochondrial inner membrane    The process comprising the import of proteins into the mitochondrion from outside the organelle and their insertion into the mitochondrial inner membrane. The translocase of the outer membrane complex mediates the passage of these proteins across the outer membrane, after which they are guided by either of two inner membrane translocase complexes into their final destination in the inner membrane.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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: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:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0042719    mitochondrial intermembrane space protein transporter complex    Soluble complex of the mitochondrial intermembrane space composed of various combinations of small Tim proteins; acts as a protein transporter to guide proteins to the Tim22 complex for insertion into the mitochondrial inner membrane.
    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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

2bsk HUMAN TIM9-TIM10 HEXAMERIC ASSEMBLY
3cjh YEAST TIM8-TIM13