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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL MTERF FRAGMENT (AA 99-399) IN COMPLEX WITH A 12-MER DNA ENCOMPASSING THE TRNALEU(UUR) BINDING SEQUENCE
 
Authors :  N. Jimenez-Menendez, P. Fernandez-Millan, A. Rubio-Cosials, C. Arna J. Montoya, H. T. Jacobs, P. Bernado, M. Coll, I. Uson, M. Sola
Date :  27 May 10  (Deposition) - 16 Jun 10  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Mitochondrial Transcription Termination Factor-Dna Complex, Mitochondrial Replication Pausing-Dna Complex, Left-Handed Helical Tandem Repeat, Protein-Dna Complex, Transcription, Replication-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Jimenez-Menendez, P. Fernandez-Millan, A. Rubio-Cosials, C. Arnan, J. Montoya, H. T. Jacobs, P. Bernado, M. Coll, I. Uson, M. Sola
Human Mitochondrial Mterf Wraps Around Dna Through A Left-Handed Superhelical Tandem Repeat.
Nat. Struct. Mol. Biol. V. 17 891 2010
PubMed-ID: 20543826  |  Reference-DOI: 10.1038/NSMB.1859

(-) Compounds

Molecule 1 - TRANSCRIPTION TERMINATION FACTOR, MITOCHONDRIAL
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 99-399
    GeneMTERF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMITOCHONDRIAL TRANSCRIPTION TERMINATION FACTOR 1, MTERF
 
Molecule 2 - DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*G)-3')
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*C)-3')
    ChainsC
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:248 , ARG A:251 , SER A:285 , ASN A:286 , ASP A:287BINDING SITE FOR RESIDUE CIT A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N7Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N7Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053785A231TMTEF1_HUMANPolymorphism17856025AA231T
2UniProtVAR_024237A294TMTEF1_HUMANPolymorphism10266424AA294T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N7Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3N7Q)

(-) 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:298
 aligned with MTEF1_HUMAN | Q99551 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:298
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
          MTEF1_HUMAN   100 MITNEQDLKMFLLSKGASKEVIASIISRYPRAITRTPENLSKRWDLWRKIVTSDLEIVNILERSPESFFRSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNPFILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKLFSLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDCLMEENISISQIIENPRVLDSSISTLKSRIKELVNAGCNLSTLNITLLSWSKKRYEAKLKKLSR 397
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------T------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n7q A 100 MITNEQDLKMFLLSKGASKEVIASIISRYPRAITRTPENLSKRWDLWRKIVTSDLEIVNILERSPESFFRSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNPFILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKLFSLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDCLMEENISISQIIENPRVLDSSISTLKSRIKELVNAGCNLSTLNITLLSWSKKRYEAKLKKLSR 397
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        

Chain B from PDB  Type:DNA  Length:12
                                            
                 3n7q B   1 GGCAGAGCCCGG  12
                                    10  

Chain C from PDB  Type:DNA  Length:12
                                            
                 3n7q C   1 CCGGGCTCTGCC  12
                                    10  

   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  (0, 0)

(no "SCOP Domain" information available for 3N7Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N7Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3N7Q)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MTEF1_HUMAN | Q99551)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    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).
biological process
    GO:0032392    DNA geometric change    The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases.
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006393    termination of mitochondrial transcription    The process in which the synthesis of an RNA molecule using a mitochondrial DNA template is completed.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0042645    mitochondrial nucleoid    The region of a mitochondrion to which the DNA is confined.
    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

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

UniProtKB/Swiss-Prot
        MTEF1_HUMAN | Q995513mva 3mvb 3n6s 5cky 5co0 5crj 5crk

(-) Related Entries Specified in the PDB File

3n6s FULL-LENGTH PROTEIN BOUND TO DNA