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- PDB-9mvr: AI-designed Cas13 anti-CRISPR AIcrVIA1 -

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Basic information

Entry
Database: PDB / ID: 9mvr
TitleAI-designed Cas13 anti-CRISPR AIcrVIA1
ComponentsAIcrVIA1
KeywordsDE NOVO PROTEIN / anti-CRISPR / Acr / CRISPR / Cas13
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsTaveneau, C. / Chai, H.X. / Knott, G.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other privateSMRF2021-276 Australia
CitationJournal: Nat Chem Biol / Year: 2026
Title: De novo design of potent CRISPR-Cas13 inhibitors.
Authors: Cyntia Taveneau / Her Xiang Chai / Jovita D'Silva / Rebecca S Bamert / Honglin Chen / Brooke K Hayes / Roland W Calvert / Jacob Purcell / Daniel J Curwen / Fabian Munder / Lisandra L Martin ...Authors: Cyntia Taveneau / Her Xiang Chai / Jovita D'Silva / Rebecca S Bamert / Honglin Chen / Brooke K Hayes / Roland W Calvert / Jacob Purcell / Daniel J Curwen / Fabian Munder / Lisandra L Martin / Jeremy J Barr / Joseph Rosenbluh / Mohamed Fareh / Rhys Grinter / Gavin J Knott /
Abstract: CRISPR-Cas systems are transformative tools for gene editing that can be tuned or controlled by anti-CRISPRs (Acrs)-phage-derived inhibitors that regulate CRISPR-Cas activity. However, Acrs that can ...CRISPR-Cas systems are transformative tools for gene editing that can be tuned or controlled by anti-CRISPRs (Acrs)-phage-derived inhibitors that regulate CRISPR-Cas activity. However, Acrs that can inhibit biotechnologically relevant CRISPR systems are relatively rare and challenging to discover. To overcome this limitation, we describe a highly successful and rapid approach that leverages de novo protein design to develop new-to-nature proteins for controlling CRISPR-Cas activity. Here, using Leptotrichia buccalis CRISPR-Cas13a as a representative example, we demonstrate that Acrs designed using artificial intelligence (AIcrs) are capable of highly potent and specific inhibition of CRISPR-Cas13a nuclease activity. We present a comprehensive workflow for design validation and demonstrate AIcr functionality in controlling CRISPR-Cas13 activity in bacterial and human cells. The ability to design bespoke inhibitors of Cas effectors will contribute to the ongoing development of CRISPR-Cas tools in diverse applications across research, medicine, agriculture and microbiology.
History
DepositionJan 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AIcrVIA1
B: AIcrVIA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4333
Polymers19,3982
Non-polymers351
Water1,47782
1
A: AIcrVIA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7342
Polymers9,6991
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AIcrVIA1


Theoretical massNumber of molelcules
Total (without water)9,6991
Polymers9,6991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.403, 62.900, 84.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein AIcrVIA1


Mass: 9698.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1M Bis-Tris propane, 2.6M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 1.94→42.46 Å / Num. obs: 25959 / % possible obs: 99.37 % / Redundancy: 6.8 % / Biso Wilson estimate: 36.74 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.036 / Net I/σ(I): 10.5
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 1300 / CC1/2: 0.66 / CC star: 0.89 / Rpim(I) all: 0.43 / % possible all: 90.36

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→42.46 Å / SU ML: 0.2407 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.7475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2463 2571 10.07 %
Rwork0.1991 22954 -
obs0.2038 25525 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.25 Å2
Refinement stepCycle: LAST / Resolution: 1.94→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 1 82 1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321280
X-RAY DIFFRACTIONf_angle_d0.56971721
X-RAY DIFFRACTIONf_chiral_restr0.0462187
X-RAY DIFFRACTIONf_plane_restr0.003220
X-RAY DIFFRACTIONf_dihedral_angle_d3.7714160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.970.35341340.32211178X-RAY DIFFRACTION90.36
1.97-2.010.32271370.26321255X-RAY DIFFRACTION100
2.02-2.060.30371430.26621266X-RAY DIFFRACTION99.72
2.06-2.110.25741480.25051299X-RAY DIFFRACTION99.93
2.11-2.160.29471490.25091290X-RAY DIFFRACTION100
2.16-2.220.27211400.22031277X-RAY DIFFRACTION99.72
2.22-2.280.26091370.21011250X-RAY DIFFRACTION99.64
2.28-2.360.26051470.20841332X-RAY DIFFRACTION100
2.36-2.440.25071390.1921259X-RAY DIFFRACTION100
2.44-2.540.18311500.19441277X-RAY DIFFRACTION99.93
2.54-2.650.23531390.21571296X-RAY DIFFRACTION100
2.65-2.790.27411430.21561292X-RAY DIFFRACTION99.93
2.79-2.970.22411470.19911269X-RAY DIFFRACTION99.86
2.97-3.20.23361460.20711268X-RAY DIFFRACTION100
3.2-3.520.23981460.19271287X-RAY DIFFRACTION99.93
3.52-4.030.22511410.17731294X-RAY DIFFRACTION100
4.03-5.060.23191450.17141273X-RAY DIFFRACTION100
5.08-42.460.27231400.19291292X-RAY DIFFRACTION99.86

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