3MXA

Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus.

Munoz, I.G.Prieto, J.Subramanian, S.Coloma, J.Redondo, P.Villate, M.Merino, N.Marenchino, M.D'Abramo, M.Gervasio, F.L.Grizot, S.Daboussi, F.Smith, J.Chion-Sotinel, I.Paques, F.Duchateau, P.Alibes, A.Stricher, F.Serrano, L.Blanco, F.J.Montoya, G.

(2011) Nucleic Acids Res 39: 729-743

  • DOI: https://doi.org/10.1093/nar/gkq801
  • Primary Citation of Related Structures:  
    2XE0, 3MX9, 3MXA, 3MXB

  • PubMed Abstract: 

    Homing endonucleases recognize long target DNA sequences generating an accurate double-strand break that promotes gene targeting through homologous recombination. We have modified the homodimeric I-CreI endonuclease through protein engineering to target a specific DNA sequence within the human RAG1 gene. Mutations in RAG1 produce severe combined immunodeficiency (SCID), a monogenic disease leading to defective immune response in the individuals, leaving them vulnerable to infectious diseases. The structures of two engineered heterodimeric variants and one single-chain variant of I-CreI, in complex with a 24-bp oligonucleotide of the human RAG1 gene sequence, show how the DNA binding is achieved through interactions in the major groove. In addition, the introduction of the G19S mutation in the neighborhood of the catalytic site lowers the reaction energy barrier for DNA cleavage without compromising DNA recognition. Gene-targeting experiments in human cell lines show that the designed single-chain molecule preserves its in vivo activity with higher specificity, further enhanced by the G19S mutation. This is the first time that an engineered meganuclease variant targets the human RAG1 locus by stimulating homologous recombination in human cell lines up to 265 bp away from the cleavage site. Our analysis illustrates the key features for à la carte procedure in protein-DNA recognition design, opening new possibilities for SCID patients whose illness can be treated ex vivo.


  • Organizational Affiliation

    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
scV3V2(G19S)362Chlamydomonas reinhardtiiMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*C)-3')B [auth C]14N/A
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')C [auth D]10N/A
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*C)-3')D [auth E]14N/A
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')E [auth F]10N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
L [auth C]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MN
Query on MN

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F [auth A],
G [auth A],
H [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
EOH
Query on EOH

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I [auth A],
J [auth A],
K [auth A]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72α = 90
b = 172.39β = 90
c = 46.53γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations