6IV8

the selenomethionine(SeMet)-derived Cas13d binary complex

• PDB DOI:  https://doi.org/10.2210/pdb6IV8/pdb
• NAKB: 6IV8

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): uncultured Ruminococcus sp.
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-12-02 Released: 2019-06-19 
• Deposition Author(s): Zhang, B., Ye, Y.M., Ye, W.W., OuYang, S.Y.
• Funding Organization(s): National Science Foundation (China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.210 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Literature

Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d.

Zhang, B., Ye, Y., Ye, W., Perculija, V., Jiang, H., Chen, Y., Li, Y., Chen, J., Lin, J., Wang, S., Chen, Q., Han, Y.S., Ouyang, S.

(2019) Nat Commun 10: 2544-2544

• PubMed: 31186424 
• DOI: https://doi.org/10.1038/s41467-019-10507-3
• Primary Citation of Related Structures:  
  6IV8, 6IV9


• PubMed Abstract: 
  

Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp. Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg ²⁺ ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA processing is executed by the HEPN-2 domain. Furthermore, both the structure and sequence of the nucleotides U(-8)-C(-1) within the repeat region are indispensable for target cleavage, and are specifically recognized by UrCas13d. Moreover, correct base pairings within two separate spacer regions (an internal and a 3'-end region) are essential for target cleavage. These findings provide a framework for the development of Cas13d into a tool for a wide range of applications.

---

Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 250.69 kDa 
• Atom Count: 16,939 
• Modelled Residue Count: 1,835 
• Deposited Residue Count: 1,964 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
The selenomethionine (SeMet)-labeled Cas13d	A, D [auth C]	930	uncultured Ruminococcus sp.	Mutation(s): 2  Gene Names: SAMEA3545300_02264

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (51-MER)	B	51	uncultured Ruminococcus sp.

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (53-MER)	C [auth D]	53	uncultured Ruminococcus sp.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth B], F [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, D [auth C]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.210 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.164	α = 90
b = 145.733	β = 90
c = 249.383	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Zhang, B., Ye, Y.M., Ye, W.W., OuYang, S.Y.

---

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31770948

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2019-06-26
  Changes: Data collection, Database references