[English] 日本語
Yorodumi
- EMDB-68245: Cryo-EM structure of AsCas12a in complex with crDNA and RNA target -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-68245
TitleCryo-EM structure of AsCas12a in complex with crDNA and RNA target
Map data
Sample
  • Complex: Cas12a
    • RNA: RNA (5'-R(P*GP*AP*CP*AP*GP*CP*CP*CP*AP*CP*AP*UP*GP*GP*CP*AP*UP*UP*CP*CP*AP*CP*U)-3')
    • Protein or peptide: CRISPR-associated endonuclease Cas12a
    • DNA: DNA (41-MER)
KeywordsCas12a / crDNA / RNA / DNA BINDING PROTEIN
Function / homology
Function and homology information


Bacillus subtilis ribonuclease / deoxyribonuclease I / deoxyribonuclease I activity / defense response to virus / lyase activity / DNA binding / RNA binding
Similarity search - Function
: / CRISPR-associated endonuclease Cpf1 REC2 domain / CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas12a
Similarity search - Component
Biological speciesAcidaminococcus sp. BV3L6 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsLam WH / Wu X / Hsing IM / Zhai Y
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Nat Biotechnol / Year: 2026
Title: DNA-guided CRISPR-Cas12a effectors for programmable RNA recognition and cleavage.
Authors: Xiaolong Wu / Wai Hei Lam / Zibin Zhao / Yumeng Cao / Haosi Lin / Xianzhen Feng / Yuanliang Zhai / I-Ming Hsing /
Abstract: CRISPR-Cas effectors typically rely on RNA guides to recognize target sequences. In Cas12a, the protospacer adjacent motif on DNA engages conserved protein residues, triggering target binding and ...CRISPR-Cas effectors typically rely on RNA guides to recognize target sequences. In Cas12a, the protospacer adjacent motif on DNA engages conserved protein residues, triggering target binding and nuclease activation. Here we reprogram Cas12a into a DNA-guided, RNA-targeting effector. Exploiting protospacer-adjacent motif-dependent interaction, we engineer synthetic CRISPR DNA that engages Cas12a to form a functional deoxyribonucleoprotein complex, while repurposing solely RNA as the programmable target. Structural, biophysical and biochemical analyses reveal the molecular basis of this DNA-guided, RNA-targeting configuration and support an activation pathway distinct from that of canonical RNA-guided systems. DNA-guided Cas12a enables direct RNA detection and efficient intracellular RNA knockdown, establishing a modular activation architecture for CRISPR-Cas12a and expanding the design space for programmable RNA manipulation.
History
DepositionJan 8, 2026-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_68245.png

Downloads & links

-
Map

FileDownload / File: emd_68245.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 240 pix.
= 252. Å		1.05 Å/pix.
x 240 pix.
= 252. Å		1.05 Å/pix.
x 240 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.092489295 - 0.21440455
Average (Standard dev.)-0.000033537883 (±0.0064952685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_68245_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_68245_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_68245_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_68245_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cas12a

EntireName: Cas12a
Components
  • Complex: Cas12a
    • RNA: RNA (5'-R(P*GP*AP*CP*AP*GP*CP*CP*CP*AP*CP*AP*UP*GP*GP*CP*AP*UP*UP*CP*CP*AP*CP*U)-3')
    • Protein or peptide: CRISPR-associated endonuclease Cas12a
    • DNA: DNA (41-MER)

-
Supramolecule #1: Cas12a

SupramoleculeName: Cas12a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acidaminococcus sp. BV3L6 (bacteria)
Molecular weightTheoretical: 156 KDa

-
Macromolecule #1: RNA (5'-R(P*GP*AP*CP*AP*GP*CP*CP*CP*AP*CP*AP*UP*GP*GP*CP*AP*UP*UP...

MacromoleculeName: RNA (5'-R(P*GP*AP*CP*AP*GP*CP*CP*CP*AP*CP*AP*UP*GP*GP*CP*AP*UP*UP*CP*CP*AP*CP*U)-3')
type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.179431 KDa
SequenceString:
GACAGCCCAC AUGGCAUUCC ACUUAUCACU GGCAUCCUUC CACUC

-
Macromolecule #2: CRISPR-associated endonuclease Cas12a

MacromoleculeName: CRISPR-associated endonuclease Cas12a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: deoxyribonuclease I
Source (natural)Organism: Acidaminococcus sp. BV3L6 (bacteria)
Molecular weightTheoretical: 151.410938 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MTQFEGFTNL YQVSKTLRFE LIPQGKTLKH IQEQGFIEED KARNDHYKEL KPIIDRIYKT YADQCLQLVQ LDWENLSAAI DSYRKEKTE ETRNALIEEQ ATYRNAIHDY FIGRTDNLTD AINKRHAEIY KGLFKAELFN GKVLKQLGTV TTTEHENALL R SFDKFTTY ...String:
MTQFEGFTNL YQVSKTLRFE LIPQGKTLKH IQEQGFIEED KARNDHYKEL KPIIDRIYKT YADQCLQLVQ LDWENLSAAI DSYRKEKTE ETRNALIEEQ ATYRNAIHDY FIGRTDNLTD AINKRHAEIY KGLFKAELFN GKVLKQLGTV TTTEHENALL R SFDKFTTY FSGFYENRKN VFSAEDISTA IPHRIVQDNF PKFKENCHIF TRLITAVPSL REHFENVKKA IGIFVSTSIE EV FSFPFYN QLLTQTQIDL YNQLLGGISR EAGTEKIKGL NEVLNLAIQK NDETAHIIAS LPHRFIPLFK QILSDRNTLS FIL EEFKSD EEVIQSFCKY KTLLRNENVL ETAEALFNEL NSIDLTHIFI SHKKLETISS ALCDHWDTLR NALYERRISE LTGK ITKSA KEKVQRSLKH EDINLQEIIS AAGKELSEAF KQKTSEILSH AHAALDQPLP TTLKKQEEKE ILKSQLDSLL GLYHL LDWF AVDESNEVDP EFSARLTGIK LEMEPSLSFY NKARNYATKK PYSVEKFKLN FQRPTLASGW DVNKEKNNGA ILFVKN GLY YLGIMPKQKG RYKALSFEPT EKTSEGFDKM YYDYFPDAAK MIPKCSTQLK AVTAHFQTHT TPILLSNNFI EPLEITK EI YDLNNPEKEP KKFQTAYAKK TGDQKGYREA LCKWIDFTRD FLSKYTKTTS IDLSSLRPSS QYKDLGEYYA ELNPLLYH I SFQRIAEKEI MDAVETGKLY LFQIYNKDFA KGHHGKPNLH TLYWTGLFSP ENLAKTSIKL NGQAELFYRP KSRMKRMAH RLGEKMLNKK LKDQKTPIPD TLYQELYDYV NHRLSHDLSD EARALLPNVI TKEVSHEIIK DRRFTSDKFL FHVPITLNYQ AANSPSKFN QRVNAYLKEH PETPIIGIDR GERNLIYITV IDSTGKILEQ RSLNTIQQFD YQKKLDNREK ERVAARQAWS V VGTIKDLK QGYLSQVIHE IVDLMIHYQA VVVLENLNFG FKSKRTGIAE KAVYQQFEKM LIDKLNCLVL KDYPAEKVGG VL NPYQLTD QFTSFAKMGT QSGFLFYVPA PYTSKIDPLT GFVDPFVWKT IKNHESRKHF LEGFDFLHYD VKTGDFILHF KMN RNLSFQ RGLPGFMPAW DIVFEKNETQ FDAKGTPFIA GKRIVPVIEN HRFTGRYRDL YPANELIALL EEKGIVFRDG SNIL PKLLE NDDSHAIDTM VALIRSVLQM RNSNAATGED YINSPVRDLN GVCFDSRFQN PEWPMDADAN GAYHIALKGQ LLLNH LKES KDLKLQNGIS NQDWLAYIQE LRN

UniProtKB: CRISPR-associated endonuclease Cas12a

-
Macromolecule #3: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.352602 KDa
SequenceString:
(DA)(DA)(DG)(DT)(DG)(DG)(DA)(DA)(DT)(DG) (DC)(DC)(DA)(DT)(DG)(DT)(DG)(DG)(DG)(DC) (DT)(DT)(DA)(DA)(DA)(DG)(DG)(DT)(DG) (DA)(DA)(DT)(DC)(DC)(DT)(DT)(DT)(DA)(DT) (DT) (DA)(DA)(DT)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationName
10.0 mMTris
50.0 mMsodium chloride

Details: 10mM Tris pH 8.0, 50mM NaCl
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2030 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1305848
CTF correctionSoftware - Name: cryoSPARC (ver. v4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8sfo

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.1) / Number images used: 54033
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.7.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 55436 / Software - Name: cryoSPARC (ver. v4.7.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

8sfo


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-22fn:
Cryo-EM structure of AsCas12a in complex with crDNA and RNA target

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more