Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 55.30 kDa 
• Atom Count: 3952 
• Residue Count: 469 
• Unique protein chains: 1

2V0R

crystal structure of a hairpin exchange variant (LTx) of the targeting LINE-1 retrotransposon endonuclease

• DOI: 10.2210/pdb2V0R/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-17 Released: 2007-07-17 
• Deposition Author(s): Repanas, K., Zingler, N., Layer, L.E., Schumann, G.G., Perrakis, A., Weichenrieder, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.272 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Determinants for DNA Target Structure Selectivity of the Human Line-1 Retrotransposon Endonuclease

Repanas, K., Zingler, N., Layer, L.E., Schumann, G.G., Perrakis, A., Weichenrieder, O.

(2007) Nucleic Acids Res 35: 4914

• PubMed: 17626046 
• DOI: 10.1093/nar/gkm516
• Primary Citation of Related Structures:  
  2V0R, 2V0S


• PubMed Abstract: 
  

The human LINE-1 endonuclease (L1-EN) is the targeting endonuclease encoded by the human LINE-1 (L1) retrotransposon. L1-EN guides the genomic integration of new L1 and Alu elements that presently account for approximately 28% of the human genome. L1-EN bears considerable technological interest, because its target selectivity may ultimately be engineered to allow the site-specific integration of DNA into defined genomic locations. Based on the crystal structure, we generated L1-EN mutants to analyze and manipulate DNA target site recognition. Crystal structures and their dynamic and functional analysis show entire loop grafts to be feasible, resulting in altered specificity, while individual point mutations do not change the nicking pattern of L1-EN. Structural parameters of the DNA target seem more important for recognition than the nucleotide sequence, and nicking profiles on DNA oligonucleotides in vitro are less well defined than the respective integration site consensus in vivo. This suggests that additional factors other than the DNA nicking specificity of L1-EN contribute to the targeted integration of non-LTR retrotransposons.

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Organizational Affiliation: 

Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LTX	A, B	240	Homo sapiens	Mutation(s): 0  EC: 2.7.7.49 (UniProt), 3.1.21 (UniProt)
Find proteins for O00370 (Homo sapiens) Explore O00370  Go to UniProtKB:  O00370

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.272 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.726	α = 90
b = 70.142	β = 90
c = 130.221	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-17 
• Released Date: 2007-07-17 
Deposition Author(s): Repanas, K., Zingler, N., Layer, L.E., Schumann, G.G., Perrakis, A., Weichenrieder, O.

Revision History 

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance