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- EMDB-65609: Structure of Csm6 from Actinomyces procaprae -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65609
TitleStructure of Csm6 from Actinomyces procaprae
Map data
Sample
  • Complex: Csm6
    • Protein or peptide: Csm6
KeywordsCsm6 / Ancillary Nuclease / Cyclic Oligoadenylate / Type III CRISPR / IMMUNE SYSTEM
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: To Be Published
Title: Structure of Csm6 from Actinomyces procaprae
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_65609.png

Downloads & links

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Map

FileDownload / File: emd_65609.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.7492967 - 6.816972
Average (Standard dev.)-0.002006374 (±0.16279063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 313.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65609_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_65609_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 : Csm6

EntireName: Csm6
Components
  • Complex: Csm6
    • Protein or peptide: Csm6

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Supramolecule #1: Csm6

SupramoleculeName: Csm6 / 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: 85.537391 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 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

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: FEI FALCON IV (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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