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- EMDB-75570: Cryo-EM structure of TccCas13a-crRNA-target RNA ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-75570
TitleCryo-EM structure of TccCas13a-crRNA-target RNA ternary complex
Map data
Sample
  • Complex: Cryo-EM structure of TccCas13a-crRNA-target RNA ternary complex
    • Protein or peptide: CRISPR-associated endoribonuclease Cas13a
    • RNA: RNA (95-MER)
KeywordsCas13a / Ternary complex / Thermostability / Structure-guided engineering / RNA BINDING PROTEIN
Function / homology
Function and homology information


endonuclease activity / defense response to virus / hydrolase activity / RNA binding
Similarity search - Function
: / Cas13a C-terminal HEPN-like domain / : / CRISPR-associated endoribonuclease Cas13a / :
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas13a
Similarity search - Component
Biological speciesThermoclostridium caenicola (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsOladeji SJ / Gao Y
Funding support United States, 2 items
OrganizationGrant numberCountry
Robert A. Welch FoundationC-2033-20230405 United States
National Science Foundation (NSF, United States)2431018 United States
CitationJournal: Cell Chem Biol / Year: 2026
Title: Structural basis and rational engineering of a thermophilic Cas13a for robust RNA detection.
Authors: Oladeji SJ / Gonzalez DH / Deng X / You Z / Zhang Y / Golla DA / Smith J / Zhang Y / Gao X / Lillehoj PB / Gao Y
History
DepositionFeb 13, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75570.png

Downloads & links

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Map

FileDownload / File: emd_75570.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0371
Minimum - Maximum-0.0017121276 - 2.0339863
Average (Standard dev.)0.0014860576 (±0.02900839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75570_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_75570_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 : Cryo-EM structure of TccCas13a-crRNA-target RNA ternary complex

EntireName: Cryo-EM structure of TccCas13a-crRNA-target RNA ternary complex
Components
  • Complex: Cryo-EM structure of TccCas13a-crRNA-target RNA ternary complex
    • Protein or peptide: CRISPR-associated endoribonuclease Cas13a
    • RNA: RNA (95-MER)

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Supramolecule #1: Cryo-EM structure of TccCas13a-crRNA-target RNA ternary complex

SupramoleculeName: Cryo-EM structure of TccCas13a-crRNA-target RNA ternary complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermoclostridium caenicola (bacteria)
Molecular weightTheoretical: 173.6 KDa

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Macromolecule #1: CRISPR-associated endoribonuclease Cas13a

MacromoleculeName: CRISPR-associated endoribonuclease Cas13a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermoclostridium caenicola (bacteria)
Molecular weightTheoretical: 143.512656 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKITKRKWGE HHPPLYFYRD EDSGRLLAQN DRKQDYTDTL FNDIAQDTFE RSLRNRLLKT PEKGDKRFYS NEIVKLVEKL CQGADVAEI MKSMERNEKL RPKNEKEIKN LKKQLDGTLS EYGKRYTAPE GAMTLNDALF YLVEGNPLKQ AMAKAELGKI R EALIKEKE ...String:
MKITKRKWGE HHPPLYFYRD EDSGRLLAQN DRKQDYTDTL FNDIAQDTFE RSLRNRLLKT PEKGDKRFYS NEIVKLVEKL CQGADVAEI MKSMERNEKL RPKNEKEIKN LKKQLDGTLS EYGKRYTAPE GAMTLNDALF YLVEGNPLKQ AMAKAELGKI R EALIKEKE NRINRVRYSI KNNKIPLRIQ EDGGITPNND RAAWLLGLMK PADPAKGITD CYPLLGELEE VFDFDKLSKT LH EKISRCQ GRPRSIAMAV DEALKQYLRE LWEKSPSRQQ DLKYYFQAVQ EYFKDNFPIR TKRMGARLRQ ELLKDKTSLS RLL EPKHMA NAVRRRLINQ STQMHILYGK LYAYCCGEDG RLLVNSETLQ RIQVHEAVKK QAMTAVLWSI SRLRYFYQFE DGDI LSNKN PIKDFRDKFL RDTNKYTHED VEACKEKLQD FFPLKELQEK IKEDAKGLQE TDNKQADTTD FKAIGHIVRD DRKLC NQLL AECVSCIGEL RHHIFHYKNV TLIQALKRIA DKVKPEDLSV LRAIYLLDRR NLKKAFAKRI SSMNLPLYYR EDLLSR IFK KEGTAFFLYS AKIQMTPSFQ RVYERGKNLR REFECERMKA EASNGQNGQD GDRLKWFRQL AAGDSADTHF NWAVEAY AE SAADVENNVE FDTDVDAQRA LRNLLKLIYR HHFLPEVQKD ETLVTGKIHK VLERNRQLSE GQGPNQGKAH GYSVIEEL Y HEGMPLSDLM KQLQRRISET ERESRELAQE KTDYAQRFIL DIFAEAFNDF LEAHYGEEYL EIMSPRKDAE AAKKWVKES KTVDLKTSID EKEPEGHLLV LYPVLRLLDH RELGELQQQM IRYRTSLASW QGESNFSEEI RIAGQIEELT ELVKLTRPEP QFAEEVWGK RAKEAFEDFI EGNMKNYEAF YLQSDNNTPV YRRNMSRLLR SGLMGVYQKV LASHKQALKR DYLLWSEKHW N VKDENGAD ISSAEQAQCL LQRLHRKYAE SPSRFTEEDC KLYEKVLRRL EDYNQAKKNL SFSSLYEICV LNLEILSRWV GF VQDWERD MYFLLLAWVR QGKLDGIKEE DVRDIFSEGN IIRNLVDTLK GENMNAFESV YFPENKGSKY LGVANDVAAL DLM RKNGWR LEAGKTCSVM EDYINRLRFL LSYDQKRMNA VTKTLQQIFD RHKVKIRFTV EKGGMLKIED VTADKIVHLK GSRL SGIEI PSHGERFIDT LKALMVYPRG

UniProtKB: CRISPR-associated endoribonuclease Cas13a

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Macromolecule #2: RNA (95-MER)

MacromoleculeName: RNA (95-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Thermoclostridium caenicola (bacteria)
Molecular weightTheoretical: 30.352959 KDa
SequenceString:
GGUCACAACU CCCAUGUAGG CGGAGACUGC AACACAAAUC UAUCUGAAUA AACUCUUCUU CCUUCUUGAA GAAGAGUUUA UUCAGAUAG AUUUGU

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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
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7303810
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 131452
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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