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

(-) Description

Title :  MOLECULAR BASIS OF ENGINEERED MEGANUCLEASE TARGETING OF THE ENDOGENOUS HUMAN RAG1 LOCUS
 
Authors :  I. G. Munoz, J. Prieto, S. Subramanian, J. Coloma, G. Montoya
Date :  07 May 10  (Deposition) - 06 Oct 10  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Protein-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. G. Munoz, J. Prieto, S. Subramanian, J. Coloma, P. Redondo, M. Villate, N. Merino, M. Marenchino, M. D'Abramo, F. L. Gervasio, S. Grizot, F. Daboussi, J. Smith, I. Chion-Sotinel, F. Paques, P. Duchateau, A. Alibes, F. Stricher, L. Serrano, F. J. Blanco, G. Montoya
Molecular Basis Of Engineered Meganuclease Targeting Of The Endogenous Human Rag1 Locus.
Nucleic Acids Res. V. 39 729 2011
PubMed-ID: 20846960  |  Reference-DOI: 10.1093/NAR/GKQ801

(-) Compounds

Molecule 1 - PROTEIN SCV3V2(G19S)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24D(+)
    Expression System StrainROSETTA(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificCHLAMYDOMONAS REINHARDTII
    Organism Taxid3055
 
Molecule 2 - DNA (5'- D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP* GP*A)-3')
    ChainsC
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    SyntheticYES
 
Molecule 3 - DNA (5'- D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP* AP*A)-3')
    ChainsD
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ACD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:20 , SER A:210 , HOH A:393 , DC C:514 , HOH D:30 , DC D:615BINDING SITE FOR RESIDUE CA A 363
2AC2SOFTWAREGLY A:19 , ASP A:211 , HOH A:372 , HOH C:4 , DC C:515 , DC D:614BINDING SITE FOR RESIDUE CA A 364

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MX9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MX9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MX9)

(-) Exons   (0, 0)

(no "Exon" information available for 3MX9)

(-) 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
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mx9 A   2 NTKYNKEFLLYLAGFVDGDGSIIAQINPNQSSKFKHRLRLTFYVTQKTQRRWFLDKLVDEIGVGYVRDSGSVSQYVLSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRASNKEFLLYLAGFVDSDGSIIAQIKPRQSNKFKHQLSLTFAVTQKTQRRWFLDKLVDEIGVGYVYDSGSVSDYRLSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 344
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336        
                                                                                                                                                                              150|                                                                                                                                                    
                                                                                                                                                                               196                                                                                                                                                    

Chain C from PDB  Type:DNA  Length:24
                                                        
                 3mx9 C 501 TTGTTCTCAGGTACCTCAGCCAGA 524
                                   510       520    

Chain D from PDB  Type:DNA  Length:24
                                                        
                 3mx9 D 601 TCTGGCTGAGGTACCTGAGAACAA 624
                                   610       620    

   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 3MX9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MX9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MX9)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3MX9)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mx9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3mx9
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3MX9)

(-) Related Entries Specified in the PDB File

3mxa 3mxb