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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN M1A58 METHYLTRANSFERASE IN A COMPLEX WITH TRNA3LYS AND SAH
 
Authors :  J. Finer-Moore, N. Czudnochowski, J. D. O'Connell Iii, A. L. Wang, R. M
Date :  01 Jul 15  (Deposition) - 04 Nov 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,N
Biol. Unit 1:  A,B,N  (2x)
Keywords :  Trna A58 Modification, Methyl Transferase-Trna Complex, Class I Methyltransferase Fold, S-Adenosyl-L-Methionine Cofactor, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Finer-Moore, N. Czudnochowski, J. D. O'Connell, A. L. Wang, R. M. Stroud
Crystal Structure Of The Human Trna M(1)A58 Methyltransferase-Trna3(Lys) Complex: Refolding Of Substrat Trna Allows Access To The Methylation Target.
J. Mol. Biol. V. 427 3862 2015
PubMed-ID: 26470919  |  Reference-DOI: 10.1016/J.JMB.2015.10.005

(-) Compounds

Molecule 1 - TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE CATALYTIC SUBUNIT TRMT61A
    Chains: A
    EC Number: 2.1.1.220
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)
    Expression System Plasmid: PET17B-6HISTRM6-TRM61
    Expression System Taxid: 469008
    Gene: TRMT61A, C14ORF172, TRM61
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRMT61A,TRNA(M1A58) MTASE SUBUNIT TRMT61A
 
Molecule 2 - TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE NON-CATALYTIC SUBUNIT TRM6
    Chains: B
    EC Number: 2.1.1.220
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)
    Expression System Plasmid: PET17B-6HISTRM6-TRM61
    Expression System Taxid: 469008
    Gene: TRMT6, KIAA1153, TRM6, CGI-09
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRM6,TRNA(M1A58)MTASE SUBUNIT TRM6
 
Molecule 3 - TRNA3LYS
    Chains: N
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABN
Biological Unit 1 (2x): ABN

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:84 , GLN A:85 , LEU A:87 , SER A:110 , GLY A:111 , THR A:112 , GLY A:113 , SER A:114 , GLY A:115 , SER A:116 , VAL A:117 , GLU A:135 , PHE A:136 , ARG A:140 , GLN A:162 , ASP A:163 , VAL A:164 , ASP A:181 , PRO A:183 , HOH A:441 , HOH A:480 , C N:56 , A N:58binding site for residue SAH A 301
2AC2SOFTWAREU N:8 , A N:9 , HOH N:211 , HOH N:249 , HOH N:255 , HOH N:276binding site for residue NA N 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CCB)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Met A:1 -Ser A:2
2Ser A:110 -Gly A:111
3Ala A:126 -Pro A:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CCB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CCB)

(-) Exons   (0, 0)

(no "Exon" information available for 5CCB)

(-) 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:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeee.....eeeee.....eeee..eeeehhhhh.......eee.....eeeee..hhhhhhh.........hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.hhh.eeee..hhhhhh........eeee...hhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhh.eeeeeeeeeeeeeeeeee..............eeeeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ccb A   1 MSFVAYEELIKEGDTAILSLGHGAMVAVRVQRGAQTQTRHGVLRHSVDLIGRPFGSKVTCGRGGWVYVLHPTPELWTLNLPHRTQILYSTDIALITMMLELRPGSVVCESGTGSGSVSHAIIRTIAPTGHLHTVEFHQQRAEKAREEFQEHRVGRWVTVRTQDVCRSGFGVSHVADAVFLDIPSPWEAVGHAWDALKVEGGRFCSFSPCIEQVQRTCQALAARGFSELSTLEVLPQVYNVRTVSLPPPDLGTGDTSPFRSGTPMKEAVGHTGYLTFATKTPG 289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  ||   267       277       287  
                                                                                                                                                                                                                                                                                      253|                            
                                                                                                                                                                                                                                                                                       261                            


Chain B from PDB  Type:PROTEIN  Length:371
                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeee.....eee....eee.hhh.........ee....ee.........................hhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......eeeeee...hhhhhhhhhhhh...eeeeee......hhhhhhh..hhhhhh.eeeee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhh.eeeeeeeeeeeeeee......eeeeee.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ccb B  18 HRIRDGDFVVLKREDVFKAVQVQRRKKVTFEKQWFYLDNVIGHSYGTAFEVTSGGSLQPKKKRKEAGTDNRNIVDDGKSQKLTQDDIKALKDKGIKGEEIVQQLIENSTTFRDKTEFAQDKYIKKKKKKYEAIITVVKPSTRILSIMYYAREPGKINHMRYDTLAQMLTLGNIRAGNKMIVMETCAGLVLGAMMERMGGFGSIIQLYPGGGPVRAATACFGFPKSFLSGLYEFPLNKVDSLLHGTFSKDYIQEKQRRQEEQRKRHLEAAALLSERNADGLIVASRFHPTPLLLSLLDFVAPSRPFVVYCQYKEPLLECYTKLRERGGVINLRLSETWLRNYQVLPDRSHPKLLMSGGGGYLLSGFTVAMDN 463
                                    27        37        47        57        67        77  ||    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264      |342       352       362       372       382       392       402       412       422       432       442       452       462 
                                                                                         80|                                                                                                                                                                                    271|                                                                                                                           
                                                                                          88                                                                                                                                                                                     340                                                                                                                           


Chain N from PDB  Type:RNA  Length:77
                                                                                                             
                 5ccb N   0 GGCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGCCA  76
                                     9        19        29        39        49        59        69
   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 5CCB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CCB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CCB)

(-) Gene Ontology  (10, 16)

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
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:126 - Pro A:127   [ RasMol ]  
    Met A:1 - Ser A:2   [ RasMol ]  
    Ser A:110 - Gly A:111   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5ccb
    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
  TRM61_HUMAN | Q96FX7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TRM6_HUMAN | Q9UJA5
    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)
  2.1.1.220
    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
  TRM61_HUMAN | Q96FX7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TRM6_HUMAN | Q9UJA5
    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
        TRM61_HUMAN | Q96FX7: 5ccx 5cd1
        TRM6_HUMAN | Q9UJA5: 5ccx 5cd1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5CCB)