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- PDB-9mvs: Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-d... -

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Basic information

Entry
Database: PDB / ID: 9mvs
TitleActivated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1
Components
  • AIcrVIA1
  • CRISPR-associated endoribonuclease Cas13a
  • Guide complementary activator RNA (aRNA)
  • crRNA
KeywordsDE NOVO PROTEIN/HYDROLASE/RNA / CRISPR / Acr / Cas13 / de novo / DE NOVO PROTEIN / DE NOVO PROTEIN-HYDROLASE-RNA complex
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA binding
Similarity search - Function
: / RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas13a
Similarity search - Component
Biological speciessynthetic construct (others)
Leptotrichia buccalis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsTaveneau, C. / Knott, G.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other privateSMRF2021-276 Australia
CitationJournal: To Be Published
Title: De novo design of potent CRISPR-Cas13 inhibitors
Authors: Taveneau, C. / Chai, X.H. / D'Silva, J. / Bamert, R.S. / Hayes, B.K. / Calvert, R.W. / Curwen, D.J. / Munder, F. / Martin, L.L. / Barr, J.J. / Grinter, R. / Knott, G.J.
History
DepositionJan 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: AIcrVIA1
A: CRISPR-associated endoribonuclease Cas13a
C: crRNA
D: Guide complementary activator RNA (aRNA)


Theoretical massNumber of molelcules
Total (without water)174,9534
Polymers174,9534
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein AIcrVIA1


Mass: 9698.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AIcrVIA1 / Source: (gene. exp.) synthetic construct (others) / Plasmid: pet29b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein CRISPR-associated endoribonuclease Cas13a / CRISPR-associated endoribonuclease C2c2 / EndoRNase / LbuC2c2


Mass: 138980.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Leptotrichia buccalis CRISPR-Cas13a / Source: (gene. exp.) Leptotrichia buccalis (bacteria) / Gene: cas13a, c2c2, Lebu_1799 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C7NBY4, Hydrolases; Acting on ester bonds
#3: RNA chain crRNA


Mass: 17743.486 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: LbuCas13 CRISPR RNA,LbuCas13 CRISPR RNA,LbuCas13 CRISPR RNA,LbuCas13 CRISPR RNA
Source: (synth.) Leptotrichia buccalis (bacteria) / References: GenBank: 257048753
#4: RNA chain Guide complementary activator RNA (aRNA)


Mass: 8530.300 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

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1COMPLEXall0MULTIPLE SOURCES
2AIcrVIA1COMPLEX#11RECOMBINANT
3LbuCas13a-crRNA-aRNACOMPLEX#2-#41MULTIPLE SOURCESTernary complex of LbuCas13a-crRNA bound to aRNA
4LbuCas13aCOMPLEX#23RECOMBINANTLeptotrichia buccalis (Lbu) CRISPR-Cas13a
5crRNA-aRNACOMPLEX#3-#43MULTIPLE SOURCESCRISPR RNA (crRNA) and activator-RNA (aRNA)
6crRNACOMPLEX#35SYNTHETICCRISPR RNA (crRNA)
7aRNACOMPLEX#45SYNTHETICactivator-RNA (aRNA)
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
33
44
55
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32synthetic construct (others)32630
54Leptotrichia buccalis (bacteria)40542
66Leptotrichia buccalis (bacteria)40542
77synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Escherichia coli BL21(DE3) (bacteria)469008
54Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
230 mMPotassium ChlorideKCl1
35 mMMagnesium ChlorideMgCl21
42 % (v/v)GlycerolC3H8O31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2544
Image scansMovie frames/image: 50 / Used frames/image: 2-50

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.5particle selection
2EPUimage acquisition
4cryoSPARC4.5.2CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARC4.5.2initial Euler assignment
10cryoSPARC4.5.2final Euler assignment
11cryoSPARC4.5.2classification
12Coot0.9.43D reconstruction
13PHENIX1.18.23D reconstruction
14PHENIX1.18.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20357 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Type: experimental model

IDPDB-IDPdb chain-IDChain-IDDetailsSource nameAccession codeInitial refinement model-ID
1BX-ray structureOther
25XWP

5xwp

AAPDB5XWP2
35XWP

5xwp

CCPDB5XWP2
45XWP

5xwp

DDPDB5XWP2
RefinementHighest resolution: 3.43 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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