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- EMDB-65610: Structure of Csm6 from Actinomyces procaprae in complex with cycl... -

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Basic information

Entry
Database: EMDB / ID: EMD-65610
TitleStructure of Csm6 from Actinomyces procaprae in complex with cyclic hexa-adenylate
Map data
Sample
  • Complex: ApCsm6-cA6 complex
    • Protein or peptide: Csm6
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
KeywordsCsm6 / Ancillary Nuclease / Allosteric activation / Cyclic Oligoadenylate / Type III CRISPR / IMMUNE SYSTEM/RNA / IMMUNE SYSTEM-RNA complex
Biological speciesActinomyces procaprae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsLin Z / Gao H / Shi R / Yang M / Liu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: EMBO J / Year: 2026
Title: Mechanistic basis for selective Csm6-2 activation by cyclic penta-adenylate in a type III CRISPR-Cas system.
Authors: Ruyi Shi / Mengquan Yang / Yusong Liu / Haishan Gao / Zhonghui Lin /
Abstract: Type III CRISPR systems generate cyclic oligoadenylate (cOA, 3 to 6 AMPs) messengers upon detecting viral RNA, activating downstream effectors to defend against viral infection. Although cOA- ...Type III CRISPR systems generate cyclic oligoadenylate (cOA, 3 to 6 AMPs) messengers upon detecting viral RNA, activating downstream effectors to defend against viral infection. Although cOA-activated effectors have been extensively characterized, the effectors specific to cA5-one of the most abundant cOA species produced during phage infection-have remained unexplored. Here, we report that the CRISPR ribonuclease Csm6 (Csm6-2) from Actinomyces procaprae selectively employs cA5 as its activator. Csm6-2 utilizes its HEPN domain, rather than the CARF domain, to mediate self-limiting cleavage of cOA activators. Cryo-EM structural analyses reveal that Csm6-2 functions as a homotetramer, and disruption of tetramer formation significantly reduces its ribonuclease activity. Although cA6 and cA5 bind Csm6-2 with comparable affinity, only cA5 induces CARF domain closure, stabilizes the tetramer, and remodels the active site in the HEPN domain. In contrast, the sixth AMP of cA6 imposes significant steric hindrance on CARF domain movement, preventing its closure and subsequent allosteric activation. These findings expand our understanding of the cOA signaling diversity and specific cOA recognition mechanisms in type III CRISPR immunity.
History
DepositionJul 30, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65610.png

Downloads & links

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Map

FileDownload / File: emd_65610.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 280 pix.
= 271.6 Å		0.97 Å/pix.
x 280 pix.
= 271.6 Å		0.97 Å/pix.
x 280 pix.
= 271.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-2.4800417 - 3.705187
Average (Standard dev.)0.0010791005 (±0.095199786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 271.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65610_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #2

Fileemd_65610_half_map_2.map
Projections & Slices
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Sample components

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Entire : ApCsm6-cA6 complex

EntireName: ApCsm6-cA6 complex
Components
  • Complex: ApCsm6-cA6 complex
    • Protein or peptide: Csm6
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')

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Supramolecule #1: ApCsm6-cA6 complex

SupramoleculeName: ApCsm6-cA6 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Actinomyces procaprae (bacteria)

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Macromolecule #1: Csm6

MacromoleculeName: Csm6 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Actinomyces procaprae (bacteria)
Molecular weightTheoretical: 85.451273 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTVLVHIVGE GDLGSDILKL KGEQRKQARH AGVTALRTAA VGGTASTPAE AVGLLLDGAA SRDHKSRFAR TPLALELGAI QAECRSGQV HVLLLGSNSG DGATADIAEA LAALLACDEV RAVLHEQYGL EVTAELRADG NLNEQVGRGD LSSWVESAYG T AADRPVVV ...String:
MTVLVHIVGE GDLGSDILKL KGEQRKQARH AGVTALRTAA VGGTASTPAE AVGLLLDGAA SRDHKSRFAR TPLALELGAI QAECRSGQV HVLLLGSNSG DGATADIAEA LAALLACDEV RAVLHEQYGL EVTAELRADG NLNEQVGRGD LSSWVESAYG T AADRPVVV SMIGGATMMC LSAMGVVDQL GYDWRLAVAG SPDDDAARLV RRGHHGDAPF YWLRALGYLE QAAAWAQEHD RE ELIDGEH SRLQGDIDAV FGSAGRDDVS SSVTDEQLAS LVAVEMARAD NGAGLAVRAW VEKHYEALLA EENADRGQDD QIS SVFKRL PGKELGKVLG MVRDEQLDQH SASAAWLLKT GDRLRPVGNR AVHDAAAPTA SELATIKNVP ELWRRVPSWM HWPG QGRVL YICGIGAGYR PPSVIERVME AGPGQELKRA VPGGMLEGGG VGEVDFLLLH SADPGSKRTA VKTCASVLLT TPKDG MIAS GVDIIDYGGV SRDQFLAVEE TSRKVAGIVR EVLETKRPSA VAVVGLGQKG AVIGALEAAQ AWCAGHAVPL FVETSV QPG QNIKQPGMQF HRIALHNDAE AALRAAAAAS LSSLNLLSAV RVLSAGDRDM DVQAQECDKL REEYLEAVNT KDPDAYA GV LLSVMETIHK LCQEAEGDVD PRLVVVVAEA VNFPRRGKKV AETLFRERYA WQGKENGYSA EWSEVDACGR GDLLRLLY E VANEVRLTHG DSSVDEAVRA VMRNRFIRIS DDFGYEGLLK RAIASVKGGA ENLGIDVDDS WAERFQALRG WAEGRS

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Macromolecule #2: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 4
Source (natural)Organism: Actinomyces procaprae (bacteria)
Molecular weightTheoretical: 1.930277 KDa
SequenceString:
AAAAAA

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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

Concentration4.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTris-HClHydroxymethyl Aminomethane Hydrochloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 667978
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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