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- EMDB-65611: Structure of Csm6 from Actinomyces procaprae in complex with cycl... -

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Basic information

Entry
Database: EMDB / ID: EMD-65611
TitleStructure of Csm6 from Actinomyces procaprae in complex with cyclic penta-adenylate
Map data
Sample
  • Complex: ApCsm6-cA5 complex
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
    • Protein or peptide: Csm6
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: 2.67 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: To Be Published
Title: Structure of Csm6 from Actinomyces procaprae in complex with cyclic penta-adenylate
Authors: Lin Z / Gao H / Shi R / Yang M / Liu Y
History
DepositionJul 30, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65611.png

Downloads & links

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Map

FileDownload / File: emd_65611.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.3166307 - 3.005591
Average (Standard dev.)-0.00019623425 (±0.06921665)
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_65611_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65611_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 : ApCsm6-cA5 complex

EntireName: ApCsm6-cA5 complex
Components
  • Complex: ApCsm6-cA5 complex
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
    • Protein or peptide: Csm6

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Supramolecule #1: ApCsm6-cA5 complex

SupramoleculeName: ApCsm6-cA5 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Actinomyces procaprae (bacteria)

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Macromolecule #1: RNA (5'-R(P*AP*AP*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*AP*A)-3') / type: rna / ID: 1 / Number of copies: 4
Source (natural)Organism: Actinomyces procaprae (bacteria)
Molecular weightTheoretical: 1.601072 KDa
SequenceString:
AAAAA

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Macromolecule #2: Csm6

MacromoleculeName: Csm6 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Actinomyces procaprae (bacteria)
Molecular weightTheoretical: 85.47032 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 AVADAAAPTA 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 VRNEVRLTHG DSSVDEAVRA VMRNRFIRIS DDFGYEGLLK RAIASVKGGA ENLGIDVDDS WAERFQALRG WAEGRS

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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 correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 143783
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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