6FB0 | pdb_00006fb0

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with its target DNA (Haemoglobin beta subunit gene) in the presence of Calcium

• PDB DOI: https://doi.org/10.2210/pdb6FB0/pdb
• NAKB: 6FB0

• Classification: DNA BINDING PROTEIN
• Organism(s): Chlamydomonas reinhardtii, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-18 Released: 2018-07-18 
• Deposition Author(s): Molina, R., Prieto, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.229 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.

Prieto, J., Redondo, P., Lopez-Mendez, B., D'Abramo, M., Merino, N., Blanco, F.J., Duchateau, P., Montoya, G., Molina, R.

(2018) Sci Rep 8: 10286-10286

• PubMed: 29980759 
• DOI: https://doi.org/10.1038/s41598-018-28599-0
• Primary Citation Related Structures: 
  6FB0, 6FB1, 6FB2, 6FB5, 6FB6, 6FB7, 6FB8, 6FB9


• PubMed Abstract: 
  

  The high DNA specificity of homing endonucleases makes them a powerful protein scaffold to engineer enzymes for genome manipulation. Understanding their molecular recognition of DNA is an important prerequisite to generate engineered enzymes able to cleave DNA in specific desired genome sites. Protein-DNA recognition studies have been mostly focused on specific direct contacts between amino acid side chains and bases to redesign the binding interface. However, the important role of indirect readout in the central region of the target DNA of the homing endonuclease I-CreI suggested that indirect readout may play a key role in the redesign of protein-DNA interactions. The sequences of the I-CreI central substrate region, 2NN, along with the adjacent 5NNN, are key for substrate cleavage. Here, we analyse the mechanism of target discrimination at the 5NNN region by the I-CreI protein, revealing its critical role in the location and occupancy of the catalytic metal ions, which is crucial for cleavage. Our data highlight the importance of indirect readout for target DNA cleavage, thus aiding I-CreI engineering when targeting new DNA sequences.

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Organizational Affiliation: 
• Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, c/Melchor Fdez. Almagro 3, 28029, Madrid, Spain.
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Cell Signalling and Adhesion Group, c/Melchor Fdez. Almagro 3, 28029, Madrid, Spain.
Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
Department of Chemistry, University of Rome "La Sapienza", Piazzale Aldo Moro 5, 00185, Rome, Italy.
CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160, Derio, Spain.
IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, 48013, Bilbao, Spain.
CELLECTIS S.A., 8 rue de la Croix Jarry, 75013, Paris, France.
Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 50.46 kDa 
• Atom Count: 3,662 
• Modeled Residue Count: 355 
• Deposited Residue Count: 355 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA endonuclease I-CreI	A	153	Chlamydomonas reinhardtii	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P05725 (Chlamydomonas reinhardtii) Explore P05725  Go to UniProtKB:  P05725

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA endonuclease I-CreI	B	154	Chlamydomonas reinhardtii	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P05725 (Chlamydomonas reinhardtii) Explore P05725  Go to UniProtKB:  P05725

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')	C [auth D]	24	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*GP*AP*GP*AP*AP*GP*TP*CP*TP*GP*A)-3')	D [auth F]	24	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGO	H [auth A], I [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
ACT	G [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	E [auth A], F [auth A], J [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.229 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.437	α = 90
b = 67.673	β = 96.75
c = 83.525	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-18 
Deposition Author(s): Molina, R., Prieto, J.

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description