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- EMDB-37219: Structure of AmCas12a with crRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-37219
TitleStructure of AmCas12a with crRNA
Map data
Sample
  • Complex: Structure of AmCas12a with crRNA
    • Protein or peptide: CRISPR-associated endonuclease Cas12a
    • RNA: RNA (44-MER)
  • Ligand: MAGNESIUM ION
KeywordsCRISPR/Cas12a / DNA binding protein / DNA BINDING PROTEIN-RNA complex
Biological speciesAnaeroglobus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFeng Y / Zhang X / Shi J / Ma P / Tang J / Huang X
Funding support China, 2 items
OrganizationGrant numberCountry
Other government2021YFA0804702
National Natural Science Foundation of China (NSFC)22177073 China
CitationJournal: Nat Commun / Year: 2025
Title: Discovery of CRISPR-Cas12a clades using a large language model.
Authors: Yuanyuan Feng / Junchao Shi / Zhanwei Li / Yongqian Li / Jiaxi Yang / Shisheng Huang / Jinfang Zheng / Wei Han / Yunbo Qiao / Jun Zhang / Qi Liu / Yao Yang / Chunyi Hu / Lina Wu / Xiaokang ...Authors: Yuanyuan Feng / Junchao Shi / Zhanwei Li / Yongqian Li / Jiaxi Yang / Shisheng Huang / Jinfang Zheng / Wei Han / Yunbo Qiao / Jun Zhang / Qi Liu / Yao Yang / Chunyi Hu / Lina Wu / Xiaokang Zhang / Jin Tang / Xingxu Huang / Peixiang Ma /
Abstract: CRISPR-Cas systems revolutionize life science. Metagenomes contain millions of unknown Cas proteins. Traditional mining relies on protein sequence alignments. In this work, we employ an evolutionary ...CRISPR-Cas systems revolutionize life science. Metagenomes contain millions of unknown Cas proteins. Traditional mining relies on protein sequence alignments. In this work, we employ an evolutionary scale language model (ESM) to learn the information beyond sequences. Trained with CRISPR-Cas data, ESM accurately identifies Cas proteins without alignment. Limited experimental data restricts feature prediction, but integrating with machine learning enables trans-cleavage activity prediction of uncharacterized Cas12a. We discover 7 undocumented Cas12a subtypes with unique CRISPR loci. Structural analyses reveal 8 subtypes of Cas1, Cas2, and Cas4. Cas12a subtypes display distinct 3D-folds. CryoEM analyses unveil unique RNA interactions with the uncharacterized Cas12a. These proteins show distinct double-strand and single-strand DNA cleavage preferences and broad PAM recognition. Finally, we establish a specific detection strategy for the oncogene SNP without traditional Cas12a PAM. This study highlights the potential of language models in exploring undocumented Cas protein function via gene cluster classification.
History
DepositionAug 18, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37219.png

Downloads & links

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Map

FileDownload / File: emd_37219.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 320 pix.
= 236.8 Å		0.74 Å/pix.
x 320 pix.
= 236.8 Å		0.74 Å/pix.
x 320 pix.
= 236.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.017328741 - 0.049475048
Average (Standard dev.)0.0001661351 (±0.0013234114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 236.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37219_msk_1.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 : Structure of AmCas12a with crRNA

EntireName: Structure of AmCas12a with crRNA
Components
  • Complex: Structure of AmCas12a with crRNA
    • Protein or peptide: CRISPR-associated endonuclease Cas12a
    • RNA: RNA (44-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Structure of AmCas12a with crRNA

SupramoleculeName: Structure of AmCas12a with crRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Anaeroglobus (bacteria)

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Macromolecule #1: CRISPR-associated endonuclease Cas12a

MacromoleculeName: CRISPR-associated endonuclease Cas12a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Anaeroglobus (bacteria)
Molecular weightTheoretical: 157.312344 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGPKKKRKVA AADYKDDDDK SRLEPGEKPY KCPECGKSFS QSGALTRHQR THTRMRTMVT FENFTKQYQV SKTLRFELIP QGKTLENMK RDGIISVDRQ RNDDYQKAKG ILDKLYKYIL DSTMETAVID WEELAIAIEE FRKSKDKKTY EKVQSKVRTA L LEHVKKQK ...String:
MGPKKKRKVA AADYKDDDDK SRLEPGEKPY KCPECGKSFS QSGALTRHQR THTRMRTMVT FENFTKQYQV SKTLRFELIP QGKTLENMK RDGIISVDRQ RNDDYQKAKG ILDKLYKYIL DSTMETAVID WEELAIAIEE FRKSKDKKTY EKVQSKVRTA L LEHVKKQK VGTEDLFKGM FSSKIITGEV LAAFPEIRLS DEENLILEKF KDFTTYFTGF FENRKNVFTD EALSTSFTYR LV NDNFIKF FDNCTVMKNV VNISPDMAKS LETCVSDLGI FPGVSLEEVF SVSFYNRLLT QTGIDQFNQL LGGISGKEGE YKK QGLNEI INLAMQQSPE VKEVLKNKAH RFTPLFKQIL SDRSTMSFIP DAFADDDEVL SAVDAYRKYL LEKNIGDRAF QLIS DIEEY SPELMRIGGK YVSVLSQLLF NSWSEIRDGV KAYKESLITG KKTKKELENI DKGIKYGVTL QEIKEALPKK DIYEE VKKY AMSVVKDYHA GLAEPLPEKI ETDDERASIK HIMDSMLGLY RFLEYFSHDS IEDTDPVFGE CLDTILDDMN ETVPLY NKV RNFSTRKVYS TEKFKLNFNN SSLANGWDKN KEQANGAVLL KKAGEYFLGI FNSKNKPKLV SDGGGGTGYE KMIYKQF PD FKKMLPKCTI SRKETKAHFQ KSDEDFTLLT DKFEKSLVIT KKIYDLGTQT VNGKKKFQVD YPRLTGDMEG YRAALKEW I DFGKKFIQAY ASTAIYDTSL FRNSSDYPDL PSFYKDVDNI CYKLTFECIP DAVINDCIDD GSLYLFKLHN KDFSAGSIG KPNLHTLYWK AIFEEENLSD VVVKLNGQAE LFYRPKSLTR PVVHEAGEVI INKTTSTGLP VPDDVYVELS KFVRNGKKGN LTDKAKNWL DKVTVRKTPH AIIKDRRFTV DKFFFHVPIT LNYKADSSPY RFNDFVRQYV KDCSDVNIIG IDRGERNLIY A VVIDGKGN IIEQRSFNTV GTYNYQEKLE QKEKERQTAR QDWATVTKIK DLKKGYLSAV VHELSKMIVK YKAIVVLENL NV GFKRMRG GIAERSVYQQ FEKALIDKLN YLVFKDEEQS GYGGVLNAYQ LTDKFESFSK MGQQTGFLFY VPAAYTSKID PLT GFINPF SWKHVKNRED RRNFLNLFSK LYYDVNTHDF VLAYHHSNKD SKYTIKGNWE IADWDILIQE NKEVFGKTGT PYCV GKRIV YMDDSTTGHN RMCAYYPHTE LKKLLSEYGI EYTSGQDLLK IIQEFDDDKL VKGLFYIIKA ALQMRNSNSE TGEDY ISSP IEGRPGICFD SRAEADTLPH NADANGAFHI AMKGLLLTER IRNDDKLAIS NEEWLNYIQE MRGASLVPRG SHHHHH HHH HH

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Macromolecule #2: RNA (44-MER)

MacromoleculeName: RNA (44-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Anaeroglobus (bacteria)
Molecular weightTheoretical: 14.125415 KDa
SequenceString:
UAAUUUCUAC UAAGUGUAGA UGACAUAUGG AAAACGAACU AUGU

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.5
GridMaterial: NICKEL/TITANIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.63 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196390
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8kgf:
Structure of AmCas12a with crRNA

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