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(-) 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 :  2.30
Chains :  Asym. Unit :  A,B,C,E,R,S,T,V
Biol. Unit 1:  A,B,C,E  (1x)
Biol. Unit 2:  R,S,T,V  (1x)
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 - V3(E8K)
    Chains: A, R
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D(+)
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
 
Molecule 2 - V2(K7E-G19S)
    Chains: B, S
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D(+)
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
 
Molecule 3 - 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')
    Chains: C, T
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synthetic: YES
 
Molecule 4 - 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')
    Chains: E, V
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCERSTV
Biological Unit 1 (1x): ABCE    
Biological Unit 2 (1x):     RSTV

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:20 , SER B:19 , HOH B:176 , HOH B:202 , DC C:514 , DC E:615BINDING SITE FOR RESIDUE CA A 175
2AC2SOFTWAREGLY A:19 , HOH A:201 , ASP B:20 , HOH C:87 , DC C:515 , DC E:614BINDING SITE FOR RESIDUE CA B 173
3AC3SOFTWARELYS A:96 , TYR B:12 , PHE B:54 , LYS B:57 , LEU B:58 , GLU B:61BINDING SITE FOR RESIDUE PO4 B 174
4AC4SOFTWAREARG A:51 , LEU B:97 , LYS B:98 , ASN B:136 , DT E:616BINDING SITE FOR RESIDUE PO4 B 175
5AC5SOFTWAREGLN B:38 , LEU B:39 , LEU B:41 , SER B:79 , DG C:503 , DT C:504BINDING SITE FOR RESIDUE PO4 C 3
6AC6SOFTWAREASP R:20 , SER S:19 , HOH S:189 , HOH S:195 , DC T:514 , DC V:615BINDING SITE FOR RESIDUE CA R 175
7AC7SOFTWAREGLY R:19 , ASP S:20 , HOH S:211 , HOH T:145 , DC T:515 , DC V:614BINDING SITE FOR RESIDUE CA S 173
8AC8SOFTWAREARG R:51 , LEU S:97 , LYS S:98 , ASN S:136 , ASP S:137 , DT V:616BINDING SITE FOR RESIDUE PO4 S 174

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MXB)

(-) 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:153
                                                                                                                                                                                         
               SCOP domains d3mxba_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee...eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mxb A   2 NTKYNKKFLLYLAGFVDGDGSIIAQINPNQSSKFKHRLRLTFYVTQKTQRRWFLDKLVDEIGVGYVRDSGSVSQYVLSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLDS 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   


Chain B from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains d3mxbb_ B: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mxb B   2 NTKYNEEFLLYLAGFVDSDGSIIAQIKPRQSNKFKHQLSLTFAVTQKTQRRWFLDKLVDEIGVGYVYDSGSVSDYRLSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLDS 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   


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


Chain E from PDB  Type:DNA  Length:24
                                                        
                 3mxb E 601 TCTGGCTGAGGTACCTGAGAACAA 624
                                   610       620    


Chain R from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains d3mxbr_ R: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mxb R   2 NTKYNKKFLLYLAGFVDGDGSIIAQINPNQSSKFKHRLRLTFYVTQKTQRRWFLDKLVDEIGVGYVRDSGSVSQYVLSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLDSL 155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    


Chain S from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains d3mxbs_ S: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mxb S   2 NTKYNEEFLLYLAGFVDSDGSIIAQIKPRQSNKFKHQLSLTFAVTQKTQRRWFLDKLVDEIGVGYVYDSGSVSDYRLSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  


Chain T from PDB  Type:DNA  Length:24
                                                        
                 3mxb T 501 TTGTTCTCAGGTACCTCAGCCAGA 524
                                   510       520    


Chain V from PDB  Type:DNA  Length:24
                                                        
                 3mxb V 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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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(-) Related Entries Specified in the PDB File

3mx9 3mxa