Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE TFB1M IN COMPLEX WITH SAM
 
Authors :  K. E. Guja, E. Yakubovskaya, H. Shi, E. Mejia, E. Hambardjieva, K. Venka A. W. Karzai, M. Garcia-Diaz
Date :  30 Jul 12  (Deposition) - 10 Jul 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Methyltransferase Fold, Rrna Methyltransferase, S-Adenosyl-L- Methionine, Methylation, Mitochondria, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Guja, K. Venkataraman, E. Yakubovskaya, H. Shi, E. Mejia, E. Hambardjieva, A. W. Karzai, M. Garcia-Diaz
Structural Basis For S-Adenosylmethionine Binding And Methyltransferase Activity By Mitochondrial Transcription Factor B1.
Nucleic Acids Res. V. 41 7947 2013
PubMed-ID: 23804760  |  Reference-DOI: 10.1093/NAR/GKT547

(-) Compounds

Molecule 1 - DIMETHYLADENOSINE TRANSFERASE 1, MITOCHONDRIAL
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ARCTIC EXPRESS RIL (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TFB1M
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MITOCHONDRIAL 12S RRNA DIMETHYLASE 1, MITOCHONDRIAL TRANSCRIPTION FACTOR B1, MTTFB1, S-ADENOSYLMETHIONINE-6-N', N'- ADENOSYL(RRNA) DIMETHYLTRANSFERASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:35 , ASN A:36 , PHE A:37 , LEU A:38 , GLY A:63 , PRO A:64 , GLY A:65 , VAL A:84 , GLU A:85 , LYS A:86 , ASP A:87 , PHE A:90 , GLY A:110 , ASP A:111 , VAL A:112 , ASN A:141 , PRO A:143 , VAL A:146 , HOH A:513BINDING SITE FOR RESIDUE SAM A 401
2AC2SOFTWARELYS A:258 , TYR A:259 , ARG A:262BINDING SITE FOR RESIDUE ACT A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GC9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GC9)

(-) Exons   (0, 0)

(no "Exon" information available for 4GC9)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh......eeeee....hhhhhhhhh....eeeee.....hhhhhhhhhhhh...eeee.............hhhhh.........eeeee..hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhh.......hhhhhhhhh.eeeeeeeeehhhhh.......eeeeeeee........hhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gc9 A  10 FRLPPLPTIREIIKLFGLRAVKQLSQNFLLDLRLTDKIVRKAGSLADVYVYEVGPGPGGITRSILNANVAELLVVEKDTRFIPGLQmLSDAAPGKLRIVHGDVLTYKIEKAFPGNIRRQWEDDPPNVHIIGNLPFSVSTPLIIKWLENISLKDGPFVYGRTKmTLTFQKEVAERLVATTGSKQHSRLSImAQYLCNVEHLFTIPGKAFVPKPKVDVGVVHLTPLIEPKIKQPFKLVEKVVQNAFQFRRKYCHRGLGmLFPEAQRLESTGRLLQLADIDPTLRPTHLSLmHFKSLCDVYRKmCDEDPQLFTYNFREELK 327
                                    19        29        39        49        59        69        79        89      | 99       109       119       129       139       149       159       169  |    179       189       199       209       219       229       239       249       259      |269       279       289       299       309|      319        
                                                                                                                 96-MSE                                                                     172-MSE                    199-MSE                                                            266-MSE                         298-MSE     310-MSE
   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 4GC9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GC9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GC9)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:218 - Pro A:219   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4gc9
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TFB1M_MOUSE | Q8JZM0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TFB1M_MOUSE | Q8JZM0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TFB1M_MOUSE | Q8JZM0: 4gc5

(-) Related Entries Specified in the PDB File

4gc5 LIGAND-FREE STRUCTURE OF TFB1M