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- EMDB-48668: Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-d... -

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Basic information

Entry
Database: EMDB / ID: EMD-48668
TitleActivated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1
Map data
Sample
  • Complex: Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1
    • Complex: AIcrVIA1
      • Protein or peptide: AIcrVIA1
    • Complex: LbuCas13a-crRNA-aRNA
      • Complex: LbuCas13a
        • Protein or peptide: CRISPR-associated endoribonuclease Cas13a
      • Complex: crRNA-aRNA
        • Complex: crRNA
          • RNA: crRNA
        • Complex: aRNA
          • RNA: Guide complementary activator RNA (aRNA)
KeywordsCRISPR / Acr / Cas13 / de novo / DE NOVO PROTEIN / DE NOVO PROTEIN-HYDROLASE-RNA complex
Function / homology: / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA binding / CRISPR-associated endoribonuclease Cas13a
Function and homology information
Biological speciessynthetic construct (others) / Leptotrichia buccalis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsTaveneau C / Knott GJ
Funding support Australia, 1 items
OrganizationGrant numberCountry
Other privateSMRF2021-276 Australia
CitationJournal: To Be Published
Title: De novo design of potent CRISPR-Cas13 inhibitors
Authors: Taveneau C / Chai XH / D'Silva J / Bamert RS / Hayes BK / Calvert RW / Curwen DJ / Munder F / Martin LL / Barr JJ / Grinter R / Knott GJ
History
DepositionJan 15, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48668.png

Downloads & links

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Map

FileDownload / File: emd_48668.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 256 pix.
= 239.59 Å		0.94 Å/pix.
x 256 pix.
= 239.59 Å		0.94 Å/pix.
x 256 pix.
= 239.59 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9359 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0441
Minimum - Maximum-0.13907124 - 0.31227598
Average (Standard dev.)-0.000047840647 (±0.009232314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 239.5904 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48668_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48668_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48668_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-d...

EntireName: Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1
Components
  • Complex: Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1
    • Complex: AIcrVIA1
      • Protein or peptide: AIcrVIA1
    • Complex: LbuCas13a-crRNA-aRNA
      • Complex: LbuCas13a
        • Protein or peptide: CRISPR-associated endoribonuclease Cas13a
      • Complex: crRNA-aRNA
        • Complex: crRNA
          • RNA: crRNA
        • Complex: aRNA
          • RNA: Guide complementary activator RNA (aRNA)

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Supramolecule #1: Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-d...

SupramoleculeName: Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: AIcrVIA1

SupramoleculeName: AIcrVIA1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: LbuCas13a-crRNA-aRNA

SupramoleculeName: LbuCas13a-crRNA-aRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4 / Details: Ternary complex of LbuCas13a-crRNA bound to aRNA

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Supramolecule #4: LbuCas13a

SupramoleculeName: LbuCas13a / type: complex / ID: 4 / Parent: 3 / Macromolecule list: #2 / Details: Leptotrichia buccalis (Lbu) CRISPR-Cas13a
Source (natural)Organism: Leptotrichia buccalis (bacteria)

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Supramolecule #5: crRNA-aRNA

SupramoleculeName: crRNA-aRNA / type: complex / ID: 5 / Parent: 3 / Macromolecule list: #3-#4 / Details: CRISPR RNA (crRNA) and activator-RNA (aRNA)

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Supramolecule #6: crRNA

SupramoleculeName: crRNA / type: complex / ID: 6 / Parent: 5 / Macromolecule list: #3 / Details: CRISPR RNA (crRNA)
Source (natural)Organism: Leptotrichia buccalis (bacteria) / Synthetically produced: Yes

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Supramolecule #7: aRNA

SupramoleculeName: aRNA / type: complex / ID: 7 / Parent: 5 / Macromolecule list: #4 / Details: activator-RNA (aRNA)
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: AIcrVIA1

MacromoleculeName: AIcrVIA1 / type: protein_or_peptide / ID: 1 / Details: AIcrVIA1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.698852 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKTIKVDVIV VGDDEELVEE YKKEAELIGK EYGVKIEVEP YFLEEGKFPW LDVDFAYNTT QEELDKAEKE AKKIAGSHHH HHH

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Macromolecule #2: CRISPR-associated endoribonuclease Cas13a

MacromoleculeName: CRISPR-associated endoribonuclease Cas13a / type: protein_or_peptide / ID: 2 / Details: Leptotrichia buccalis CRISPR-Cas13a / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Leptotrichia buccalis (bacteria)
Molecular weightTheoretical: 138.980594 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SNAMKVTKVG GISHKKYTSE GRLVKSESEE NRTDERLSAL LNMRLDMYIK NPSSTETKEN QKRIGKLKKF FSNKMVYLKD NTLSLKNGK KENIDREYSE TDILESDVRD KKNFAVLKKI YLNENVNSEE LEVFRNDIKK KLNKINSLKY SFEKNKANYQ K INENNIEK ...String:
SNAMKVTKVG GISHKKYTSE GRLVKSESEE NRTDERLSAL LNMRLDMYIK NPSSTETKEN QKRIGKLKKF FSNKMVYLKD NTLSLKNGK KENIDREYSE TDILESDVRD KKNFAVLKKI YLNENVNSEE LEVFRNDIKK KLNKINSLKY SFEKNKANYQ K INENNIEK VEGKSKRNII YDYYRESAKR DAYVSNVKEA FDKLYKEEDI AKLVLEIENL TKLEKYKIRE FYHEIIGRKN DK ENFAKII YEEIQNVNNM KELIEKVPDM SELKKSQVFY KYYLDKEELN DKNIKYAFCH FVEIEMSQLL KNYVYKRLSN ISN DKIKRI FEYQNLKKLI ENKLLNKLDT YVRNCGKYNY YLQDGEIATS DFIARNRQNE AFLRNIIGVS SVAYFSLRNI LETE NENDI TGRMRGKTVK NNKGEEKYVS GEVDKIYNEN KKNEVKENLK MFYSYDFNMD NKNEIEDFFA NIDEAISSIR HGIVH FNLE LEGKDIFAFK NIAPSEISKK MFQNEINEKK LKLKIFRQLN SANVFRYLEK YKILNYLKRT RFEFVNKNIP FVPSFT KLY SRIDDLKNSL GIYWKTPKTN DDNKTKEIID AQIYLLKNIY YGEFLNYFMS NNGNFFEISK EIIELNKNDK RNLKTGF YK LQKFEDIQEK IPKEYLANIQ SLYMINAGNQ DEEEKDTYID FIQKIFLKGF MTYLANNGRL SLIYIGSDEE TNTSLAEK K QEFDKFLKKY EQNNNIKIPY EINEFLREIK LGNILKYTER LNMFYLILKL LNHKELTNLK GSLEKYQSAN KEEAFSDQL ELINLLNLDN NRVTEDFELE ADEIGKFLDF NGNKVKDNKE LKKFDTNKIY FDGENIIKHR AFYNIKKYGM LNLLEKIADK AGYKISIEE LKKYSNKKNE IEKNHKMQEN LHRKYARPRK DEKFTDEDYE SYKQAIENIE EYTHLKNKVE FNELNLLQGL L LRILHRLV GYTSIWERDL RFRLKGEFPE NQYIEEIFNF ENKKNVKYKG GQIVEKYIKF YKELHQNDEV KINKYSSANI KV LKQEKKD LYIRNYIAHF NYIPHAEISL LEVLENLRKL LSYDRKLKNA VMKSVVDILK EYGFVATFKI GADKKIGIQT LES EKIVHL KNLKKKKLMT DRNSEELCKL VKIMFEYKME EKKSEN

UniProtKB: CRISPR-associated endoribonuclease Cas13a

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Macromolecule #3: crRNA

MacromoleculeName: crRNA / type: rna / ID: 3
Details: LbuCas13 CRISPR RNA,LbuCas13 CRISPR RNA,LbuCas13 CRISPR RNA,LbuCas13 CRISPR RNA
Number of copies: 1
Source (natural)Organism: Leptotrichia buccalis (bacteria)
Molecular weightTheoretical: 17.743486 KDa
SequenceString:
UAGACCACCC CAAAAAUGAA GGGGACUAAA ACUUUCUUUC UUUCCUUUUU CUGCCG

GENBANK: GENBANK: CP001685.1

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Macromolecule #4: Guide complementary activator RNA (aRNA)

MacromoleculeName: Guide complementary activator RNA (aRNA) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.5303 KDa
SequenceString:
CGGCAGAAAA AGGAAAGAAA GAAACC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mMTris
30.0 mMPotassium ChlorideKCl
5.0 mMMagnesium ChlorideMgCl2
2.0 % (v/v)GlycerolC3H8O3
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 2-50 / Number real images: 2544 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xwp


Details: LbuCas13a-crRNA-aRNA complex
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Coot (ver. 0.9.4), PHENIX (ver. 1.18.2)) / Number images used: 20357
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.2)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.5.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
chain_id: B, source_name: Other, initial_model_type: experimental modelX-ray structure
chain_id: A, source_name: PDB, initial_model_type: experimental model

5xwp

chain_id: C, source_name: PDB, initial_model_type: experimental model

5xwp

chain_id: D, source_name: PDB, initial_model_type: experimental model

5xwp

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9mvs:
Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1

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