8UMF | pdb_00008umf

Structure of PsCas9 in complex with gRNA and DNA in product state

• PDB DOI: https://doi.org/10.2210/pdb8UMF/pdb
• NAKB: 8UMF
• EM Map EMD-42378: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Parasutterella secunda, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-17 Released: 2024-10-02 
• Deposition Author(s): Bravo, J.P.K., Taylor, D.W.
• Funding Organization(s): Welch Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-guided engineering of PsCas9 yields a high fidelity and activity enzyme for in vivo gene editing

Bravo, J.P.K., Taylor, D.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 284.21 kDa 
• Atom Count: 14,804 
• Modeled Residue Count: 1,549 
• Deposited Residue Count: 1,833 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas9	A	1,462	Parasutterella secunda	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (121-MER)	B	131	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (80-MER)	C	80	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (80-MER)	D, E	80	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Bravo, J.P.K., Taylor, D.W.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	F-1938
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM138348

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release
  
• Version 1.1: 2025-05-14
  Changes: Data collection, Structure summary