5XWP

Crystal structure of LbuCas13a-crRNA-target RNA ternary complex

• PDB DOI:  https://doi.org/10.2210/pdb5XWP/pdb
• NAKB: 5XWP

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Leptotrichia buccalis C-1013-b, synthetic construct
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2017-06-30 Released: 2017-09-13 
• Deposition Author(s): Liu, L., Li, X., Li, Z., Wang, Y.
• Funding Organization(s): Ministry of Science and Technology (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.09 Å
• R-Value Free: 0.244 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a.

Liu, L., Li, X., Ma, J., Li, Z., You, L., Wang, J., Wang, M., Zhang, X., Wang, Y.

(2017) Cell 170: 714-726.e10

• PubMed: 28757251 
• DOI: https://doi.org/10.1016/j.cell.2017.06.050
• Primary Citation of Related Structures:  
  5XWP, 5XWY


• PubMed Abstract: 
  

Cas13a, a type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, degrades invasive RNAs targeted by CRISPR RNA (crRNA) and has potential applications in RNA technology. To understand how Cas13a is activated to cleave RNA, we have determined the crystal structure of Leptotrichia buccalis (Lbu) Cas13a bound to crRNA and its target RNA, as well as the cryo-EM structure of the LbuCas13a-crRNA complex. The crRNA-target RNA duplex binds in a positively charged central channel of the nuclease (NUC) lobe, and Cas13a protein and crRNA undergo a significant conformational change upon target RNA binding. The guide-target RNA duplex formation triggers HEPN1 domain to move toward HEPN2 domain, activating the HEPN catalytic site of Cas13a protein, which subsequently cleaves both single-stranded target and collateral RNAs in a non-specific manner. These findings reveal how Cas13a of type VI CRISPR-Cas systems defend against RNA phages and set the stage for its development as a tool for RNA manipulation.

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Organizational Affiliation: 

Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 336.35 kDa 
• Atom Count: 21,838 
• Modelled Residue Count: 2,414 
• Deposited Residue Count: 2,498 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, F [auth B]	1,160	Leptotrichia buccalis C-1013-b	Mutation(s): 2  Gene Names: Lebu_1799, cas13a, c2c2 EC: 3.1
UniProt
Find proteins for C7NBY4 (Leptotrichia buccalis (strain ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b)) Explore C7NBY4  Go to UniProtKB:  C7NBY4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (59-MER)	B [auth C], D [auth E]	59	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (30-MER)	C [auth D], E [auth F]	30	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.09 Å
• R-Value Free: 0.244 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.576	α = 90
b = 132.87	β = 90.8
c = 139.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Liu, L., Li, X., Li, Z., Wang, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2014CB910102

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Author supporting evidence