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

(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE METHYLTRANSFERASE DOMAIN OF BACTERIAL-AVHEN1-CN
 
Authors :  R. H. Huang, C. M. Chan, C. Zhou, J. S. Brunzelle
Date :  18 Sep 09  (Deposition) - 20 Oct 09  (Release) - 10 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Mui Chan, C. Zhou, J. S. Brunzelle, R. H. Huang
Structural And Biochemical Insights Into 2'-O-Methylation At The 3'-Terminal Nucleotide Of Rna By Hen1.
Proc. Natl. Acad. Sci. Usa V. 106 17699 2009
PubMed-ID: 19822745  |  Reference-DOI: 10.1073/PNAS.0907540106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEN1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 262-461
    Gene: AVA_1594
    Organism Scientific: ANABAENA VARIABILIS
    Organism Taxid: 240292
    Strain: ATCC 29413 / PCC 7937

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3JWJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp B:446 -Pro B:447

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JWJ)

(-) 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:188
 aligned with Q3MCR9_ANAVT | Q3MCR9 from UniProtKB/TrEMBL  Length:461

    Alignment length:199
                                   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452         
         Q3MCR9_ANAVT   263 SLNQQRMNGVVAALKQSNARRVIDLGCGQGNLLKILLKDSFFEQITGVDVSYRSLEIAQERLDRLRLPRNQWERLQLIQGALTYQDKRFHGYDAATVIEVIEHLDLSRLGAFERVLFEFAQPKIVIVTTPNIEYNVKFANLPAGKLRHKDHRFEWTRSQFQNWANKITERFAYNVQFQPIGEADPEVGSPTQMAVFIHR 461
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhh.....eeeeee.hhhhhhhhhhhhhh...hhhhhh.eeeee......hhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhhh.-----------.....hhhhhhhhhhhhhhhh.eeeeeeee..........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jwj A 263 SLNQQRMNGVVAALKQSNARRVIDLGCGQGNLLKILLKDSFFEQITGVDVSYRSLEIAQERLDRLRLPRNQWERLQLIQGALTYQDKRFHGYDAATVIEVIEHLDLSRLGAFERVLFEFAQPKIVIVTTPNIEYNVKFA-----------HRFEWTRSQFQNWANKITERFAYNVQFQPIGEADPEVGSPTQMAVFIHR 461
                                   272       282       292       302       312       322       332       342       352       362       372       382       392        |-         -|      422       432       442       452         
                                                                                                                                                                    401         413                                                


Chain B from PDB  Type:PROTEIN  Length:189
 aligned with Q3MCR9_ANAVT | Q3MCR9 from UniProtKB/TrEMBL  Length:461

    Alignment length:200
                                   271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461
         Q3MCR9_ANAVT   262 ISLNQQRMNGVVAALKQSNARRVIDLGCGQGNLLKILLKDSFFEQITGVDVSYRSLEIAQERLDRLRLPRNQWERLQLIQGALTYQDKRFHGYDAATVIEVIEHLDLSRLGAFERVLFEFAQPKIVIVTTPNIEYNVKFANLPAGKLRHKDHRFEWTRSQFQNWANKITERFAYNVQFQPIGEADPEVGSPTQMAVFIHR 461
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Methyltransf_23-3jwjB01 B:262-429                                                                                                                                       -------------------------------- Pfam domains (1)
           Pfam domains (2) Methyltransf_23-3jwjB02 B:262-429                                                                                                                                       -------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhh.....eeeeee.hhhhhhhhhhhhhh......hhh.eeeee......hhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhh..-----------.....hhhhhhhhhhhhhhhh.eeeee.............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jwj B 262 ISLNQQRMNGVVAALKQSNARRVIDLGCGQGNLLKILLKDSFFEQITGVDVSYRSLEIAQERLDRLRLPRNQWERLQLIQGALTYQDKRFHGYDAATVIEVIEHLDLSRLGAFERVLFEFAQPKIVIVTTPNIEYNVKFA-----------HRFEWTRSQFQNWANKITERFAYNVQFQPIGEADPEVGSPTQMAVFIHR 461
                                   271       281       291       301       311       321       331       341       351       361       371       381       391       401         - |     421       431       441       451       461
                                                                                                                                                                     401         413
   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 3JWJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q3MCR9_ANAVT | Q3MCR9)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0008173    RNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
biological process
    GO:0001510    RNA methylation    Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor.

 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
(no "Ligands, Modified Residues, Ions" information available for 3jwj)
 
  Sites
(no "Sites" information available for 3jwj)
 
  Cis Peptide Bonds
    Asp B:446 - Pro B:447   [ 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 | Biol. Unit 1 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
  3jwj
    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
  Q3MCR9_ANAVT | Q3MCR9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q3MCR9_ANAVT | Q3MCR9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q3MCR9_ANAVT | Q3MCR9: 3jwh

(-) Related Entries Specified in the PDB File

3jwg 3jwh 3jwi