9NVU | pdb_00009nvu

Engineered OrufIscB-omegaRNA-target DNA complex

• PDB DOI: https://doi.org/10.2210/pdb9NVU/pdb
• NAKB: 9NVU
• EM Map EMD-49856: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA/DNA
• Organism(s): synthetic construct, metagenome
• Expression System: synthetic construct, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-21 Released: 2025-05-21 
• Deposition Author(s): Xu, P., Zhu, S., Zhang, F.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Evolution-guided protein design of IscB for persistent epigenome editing in vivo.

Kannan, S., Altae-Tran, H., Zhu, S., Xu, P., Strebinger, D., Oshiro, R., Faure, G., Moeller, L., Pham, J., Mears, K.S., Ni, H.M., Macrae, R.K., Zhang, F.

(2025) Nat Biotechnol 

• PubMed: 40335752 
• DOI: https://doi.org/10.1038/s41587-025-02655-3
• Primary Citation of Related Structures:  
  9NVU


• PubMed Abstract: 
  

  Naturally existing enzymes have been adapted for a variety of molecular technologies, with enhancements or modifications to the enzymes introduced to improve the desired function; however, it is difficult to engineer variants with enhanced activity while maintaining specificity. Here we engineer the compact Obligate Mobile Element Guided Activity (OMEGA) RNA-guided endonuclease IscB and its guiding RNA (ωRNA) by combining ortholog screening, structure-guided protein domain design and RNA engineering, and deep learning-based structure prediction to generate an improved variant, NovaIscB. We show that the compact NovaIscB achieves up to 40% indel activity (~100-fold improvement over wild-type OgeuIscB) on the human genome with improved specificity relative to existing IscBs. We further show that NovaIscB can be fused with a methyltransferase to create a programmable transcriptional repressor, OMEGAoff, that is compact enough to be packaged in a single adeno-associated virus vector for persistent in vivo gene repression. This study highlights the power of combining natural diversity with protein engineering to design enhanced enzymes for molecular biology applications.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Cambridge, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Yang Tan Collective, Cambridge, MA, USA.
Howard Hughes Medical Institute, Cambridge, MA, USA. [e-mail].
Broad Institute of MIT and Harvard, Cambridge, MA, USA. [e-mail].
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA. [e-mail].
Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA. [e-mail].
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. [e-mail].
Yang Tan Collective, Cambridge, MA, USA. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 163.46 kDa 
• Atom Count: 9,655 
• Modeled Residue Count: 831 
• Deposited Residue Count: 898 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
OrufIscB-REC-swap 49	B [auth P]	603	metagenome	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
NTS	A [auth N]	29	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA TS	C [auth T]	39	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (162-MER)	D [auth W]	227	metagenome

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth P], H [auth P]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth P], F [auth P], I [auth T], J [auth W]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Xu, P., Zhu, S., Zhang, F.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release