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(-) Description

Title :  YEAST TIM44 C-TERMINAL DOMAIN COMPLEXED WITH CYMAL-3
 
Authors :  W. Cui, R. Josyula, Z. Fu, B. Sha
Date :  31 Jan 11  (Deposition) - 09 Mar 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Keywords :  Mitochondrion, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Cui, R. Josyula, J. Li, Z. Fu, B. Sha
Membrane Binding Mechanism Of Yeast Mitochondrial Periphera Membrane Protein Tim44.
Protein Pept. Lett. V. 18 718 2011
PubMed-ID: 21342097

(-) Compounds

Molecule 1 - MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM44
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 210-431
    GeneTIM44, ISP45, MIM44, MPI1, YIL022W
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymINNER MEMBRANE IMPORT SITE PROTEIN 45, ISP45, MEMBRANE IMPORT MACHINERY PROTEIN MIM44, MITOCHONDRIAL PROTEIN IMPORT PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:246 , ARG B:428BINDING SITE FOR RESIDUE CL B 1
2AC2SOFTWAREARG A:428 , SER B:427 , GLN B:429BINDING SITE FOR RESIDUE CL A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QK9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QK9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QK9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QK9)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIL022W1YIL022W.1IX:311163-3124581296TIM44_YEAST1-4314312A:236-431 (gaps)
B:235-431 (gaps)
196
197

(-) 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:174
 aligned with TIM44_YEAST | Q01852 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:196
                                   245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425      
          TIM44_YEAST   236 QSLKNKLWDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPEILEAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDIPVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTRDPEQIDDDETEGWKILEFVRGGSRQFT 431
               SCOP domains d3qk9a_ A: automated mat         ches                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.hhhhhhhhhhh.---------.hhhhhh...-----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eeeeeeeeeeeeeee......eeeeeeeeeeee..eee..............eeeeeeeeeee..--------..eeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:236-431 (gaps) UniProt: 1-431 [INCOMPLETE]                                                                                                                                          Transcript 1
                 3qk9 A 236 QSLKNKLWDESENPLIVVMRKITN---------ESSRVYSQFK-----FSNESFTRHLREYIVPEILEAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDIPVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTRDP--------EGWKILEFVRGGSRQFT 431
                                   245       255   |     -   |   275  |    285       295       305       315       325       335       345       355       365       375       385       395       405|      415       425      
                                                 259       269      278   284                                                                                                                       406      415                

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with TIM44_YEAST | Q01852 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:197
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       
          TIM44_YEAST   235 IQSLKNKLWDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPEILEAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDIPVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTRDPEQIDDDETEGWKILEFVRGGSRQFT 431
               SCOP domains d3qk9b_ B: automated matc         hes                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------         -Tim44-3qk     9B01 B:270-424                                                                                                                               ------- Pfam domains (1)
           Pfam domains (2) -------------------------         -Tim44-3qk     9B02 B:270-424                                                                                                                               ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhh...hhhhhhhhhhhh---------.hhhhhh...-----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee.....eeee.....eeeeeeeeeee..--------..eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:235-431 (gaps) UniProt: 1-431 [INCOMPLETE]                                                                                                                                           Transcript 1
                 3qk9 B 235 IQSLKNKLWDESENPLIVVMRKITN---------ESSRVYSQFK-----FSNESFTRHLREYIVPEILEAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDIPVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTRDP--------EGWKILEFVRGGSRQFT 431
                                   244       254    |    -    |  274   |   284       294       304       314       324       334       344       354       364       374       384       394       404 |       -|      424       
                                                  259       269      278   284                                                                                                                       406      415                

   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 3QK9)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NTF2 (66)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TIM44_YEAST | Q01852)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
    GO:0030150    protein import into mitochondrial matrix    The import of proteins across the outer and inner mitochondrial membranes into the matrix. Unfolded proteins enter the mitochondrial matrix with a chaperone protein; the information required to target the precursor protein from the cytosol to the mitochondrial matrix is contained within its N-terminal matrix-targeting sequence. Translocation of precursors to the matrix occurs at the rare sites where the outer and inner membranes are close together.
    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: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.
    GO:0001405    presequence translocase-associated import motor    Protein complex located on the matrix side of the mitochondrial inner membrane and associated with the presequence translocase complex; hydrolyzes ATP to provide the force to drive import of proteins into the mitochondrial matrix.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TIM44_YEAST | Q018522fxt

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