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- PDB-5xwy: Electron cryo-microscopy structure of LbuCas13a-crRNA binary complex -

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Basic information

Entry
Database: PDB / ID: 5xwy
TitleElectron cryo-microscopy structure of LbuCas13a-crRNA binary complex
Components
  • A type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, Cas13a
  • RNA (59-MER)
KeywordsRNA BINDING PROTEIN/RNA / Cas13a / CRISPR / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology: / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas13a
Function and homology information
Biological speciesLeptotrichia buccalis (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang, X. / Wang, Y. / Ma, J. / Liu, L. / Li, X. / Li, Z. / You, L. / Wang, J. / Wang, M.
Funding support China, 3items
OrganizationGrant numberCountry
the Chinese Ministry of Science and Technology2014CB910102 China
the Natural Science Foundation of China91440201, 31571335, 31400640, 31570874 China
the Strategic Priority Research Program of the Chinese Academy of SciencesXDB08010203 China
CitationJournal: Cell / Year: 2017
Title: The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a.
Authors: Liang Liu / Xueyan Li / Jun Ma / Zongqiang Li / Lilan You / Jiuyu Wang / Min Wang / Xinzheng Zhang / Yanli Wang /
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 ...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.
History
DepositionJun 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.0Sep 13, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 13, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 13, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 13, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 13, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 13, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 13, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Other / Refinement description / Category: cell / refine / Item: _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: A type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, Cas13a
B: RNA (59-MER)


Theoretical massNumber of molelcules
Total (without water)157,4252
Polymers157,4252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-71 kcal/mol
Surface area56350 Å2

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Components

#1: Protein A type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, Cas13a


Mass: 138555.156 Da / Num. of mol.: 1 / Mutation: R1048A, H1053A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia buccalis (strain ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b) (bacteria)
Strain: ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b
Gene: Lebu_1799 / Production host: Escherichia coli (E. coli) / References: UniProt: C7NBY4
#2: RNA chain RNA (59-MER)


Mass: 18869.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: LbuCas13a-crRNA binary complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Leptotrichia buccalis (bacteria) / Strain: ATCC 14201
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2411: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 238758 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0110528
ELECTRON MICROSCOPYf_angle_d1.20114384
ELECTRON MICROSCOPYf_dihedral_angle_d11.7718615
ELECTRON MICROSCOPYf_chiral_restr0.0631619
ELECTRON MICROSCOPYf_plane_restr0.0051642

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