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- EMDB-9708: Cryo-EM structure of Csm effector complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9708
TitleCryo-EM structure of Csm effector complex
Map data
Sample
  • Complex: ToCsm effector complex
    • Protein or peptide: Csm1
    • Protein or peptide: Csm2
    • Protein or peptide: Csm3
    • Protein or peptide: Csm4
    • Protein or peptide: Csm5
    • RNA: RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP*UP*C)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsCryo-EM structure / CRISPR / Csm / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


exonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / ATP binding / identical protein binding
Similarity search - Function
CRISPR-associated protein Csm5 / CRISPR-associated protein, Csm2 Type III-A / Csm2 Type III-A / : / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : ...CRISPR-associated protein Csm5 / CRISPR-associated protein, Csm2 Type III-A / Csm2 Type III-A / : / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / Cas10/Cmr2, second palm domain / : / CRISPR type III-associated protein / RAMP superfamily / HD domain profile. / HD domain / GGDEF domain profile. / GGDEF domain / HD domain / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / CRISPR system Cms protein Csm2 / CRISPR system Cms endoribonuclease Csm3 / CRISPR system Cms protein Csm4 / CRISPR system Cms protein Csm5
Similarity search - Component
Biological speciesThermococcus onnurineus NA1 (archaea) / Thermococcus onnurineus (strain NA1) (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsHuo Y / Li T
Funding support China, 2 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08010301 China
National Science Foundation (China)31670750 China
CitationJournal: Cell Res / Year: 2018
Title: Cryo-EM structure of Type III-A CRISPR effector complex.
Authors: Yangao Huo / Tao Li / Nan Wang / Qinghua Dong / Xiangxi Wang / Tao Jiang /
History
DepositionNov 9, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJan 16, 2019-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6iqw
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9708.png

Downloads & links

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Map

FileDownload / File: emd_9708.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.27 / Movie #1: 4
Minimum - Maximum-13.652025999999999 - 21.464327000000001
Average (Standard dev.)-0.007533303 (±1.2889774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-13.65221.464-0.008

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Supplemental data

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Sample components

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Entire : ToCsm effector complex

EntireName: ToCsm effector complex
Components
  • Complex: ToCsm effector complex
    • Protein or peptide: Csm1
    • Protein or peptide: Csm2
    • Protein or peptide: Csm3
    • Protein or peptide: Csm4
    • Protein or peptide: Csm5
    • RNA: RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP*UP*C)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: ToCsm effector complex

SupramoleculeName: ToCsm effector complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Thermococcus onnurineus NA1 (archaea)

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Macromolecule #1: Csm1

MacromoleculeName: Csm1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 88.131898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEIDELTALG GLLHDIGKPV QRAGLYSGDH STQGARFLRD LAENTGRAEY ELLSLFSEFH HKGHMKNDEL MIRRIKELSP ERFGLTMED VLNALWIVYE ADNLASGERE EGQPQASRPL YSVFNPGKAY PWAELDFEKE LPVPGDVFSI RSQDYRELVK R LWEELSKA ...String:
MEIDELTALG GLLHDIGKPV QRAGLYSGDH STQGARFLRD LAENTGRAEY ELLSLFSEFH HKGHMKNDEL MIRRIKELSP ERFGLTMED VLNALWIVYE ADNLASGERE EGQPQASRPL YSVFNPGKAY PWAELDFEKE LPVPGDVFSI RSQDYRELVK R LWEELSKA KLRSDRLLPV LEKYLTFVSS VTSEGNIISL YDHMRMTSAI ALAMLRAGCT AEDVRSGRCR KEKRFLLIEG DF SGIQDFI YRVSGKGTLK YLRARSAYLE LIGWDVVLEI LSRLGLTRAN VVFNAGGHFM IIAQNTPDAV KELEEIRAKA VEW LYREFE SDLYLAIEWE PVSGREFGRE GGKNLFAEAR KRLKHKLTVR KLKRFGEIKG LFEHGHTERL AECPVCGREL PEGK LEPSA SDPETKVCPT CNRLVSLGGN LPKLLGFGRT AKNDAGVLVE GPFSGFVPYL QGGRPVGEQI LVKNTLNPGE IPESA QFVP YFVADYFKKD PKGGVATFEE LSMASTGTRR LGVMKGDVDR LGEFFSSMDS PSKLATASRF MDYFFKGYIG AIIEGK FGY IIGDVPSLRD WPEEPDIVVV YAGGDDFFIV GAWDQIFELA FRVRRAFNAY TGGKLTLSVG LGYFDERTPI YRMADVV SE RLDTAKDEGR NRVFVVGRSR PLDGKHKLSY EWNHYEELWR TYAPRIYAGN GRLKGKLESK KGLLWKLLEI RELYVRDP N DVRWAYLTAY LLGRHGLSDL FPELVGIDTK AVERKEPQPV YWVDGVLKIV LMAVRR

UniProtKB: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)

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Macromolecule #2: Csm2

MacromoleculeName: Csm2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 22.410691 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHVIF VAYHQKHGGY GRGGYGRQDR PQVDASRLFG ESPDVVGIKK MLEGKGKQWE AIQPYFDNVV REAKNFLEWS PNKRLANAV TVAAYLTSQG LKTNQVRKIL DMARTTELKV KRGEGDIKDD LVKMRYLLAY TVGKATGQSK YSLDAFHRIL D PMLEVLMG ...String:
MHHHHHHVIF VAYHQKHGGY GRGGYGRQDR PQVDASRLFG ESPDVVGIKK MLEGKGKQWE AIQPYFDNVV REAKNFLEWS PNKRLANAV TVAAYLTSQG LKTNQVRKIL DMARTTELKV KRGEGDIKDD LVKMRYLLAY TVGKATGQSK YSLDAFHRIL D PMLEVLMG SPKKENFEKF YDFLQAVVAY HKFFGGGD

UniProtKB: CRISPR system Cms protein Csm2

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Macromolecule #3: Csm3

MacromoleculeName: Csm3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 32.721936 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDRRFYGKIV IKGKIKAVTG LHIGSQRDIS EIGGIDNPVI KDPHTGLPYI PGSSLKGRLR SLFEILVNSR LGEWREKYPS LANYSPGSC RPDNQENCGK FFNRKINRGW IHVCPDYETA LACPVCRLFG ASGKESNFPS RIIVRDAFLT KEWEEKWRAG E AITEAKIE ...String:
MDRRFYGKIV IKGKIKAVTG LHIGSQRDIS EIGGIDNPVI KDPHTGLPYI PGSSLKGRLR SLFEILVNSR LGEWREKYPS LANYSPGSC RPDNQENCGK FFNRKINRGW IHVCPDYETA LACPVCRLFG ASGKESNFPS RIIVRDAFLT KEWEEKWRAG E AITEAKIE VGIDRVTSQA NPRTNERVVA GAEFEFEIIY NVENTTHWRD DIKNLLTAMA LLEDSYLGGS GSRGYGKVKF IF DSFEFRP LDYYRTGKDE DIVSIDAREK SVSDILSGFD SLFSEVEGKL EAG

UniProtKB: CRISPR system Cms endoribonuclease Csm3

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Macromolecule #4: Csm4

MacromoleculeName: Csm4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 32.345061 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPKFIAVKLI PKGPFRDIPR ADTLFGAIGN AISAIHGQSA VEELVDAFVG GARISSAFPY SGDTYYLPKP LSVEPALEGI LTGLDEEER YTTAKRLRKA KYLDLKNFEL ALRLRPFTIP EEIPYARVDV PRVVLDRVTQ DSSIYFWEEI RFREKSGVYF L YSGPREVF ...String:
MPKFIAVKLI PKGPFRDIPR ADTLFGAIGN AISAIHGQSA VEELVDAFVG GARISSAFPY SGDTYYLPKP LSVEPALEGI LTGLDEEER YTTAKRLRKA KYLDLKNFEL ALRLRPFTIP EEIPYARVDV PRVVLDRVTQ DSSIYFWEEI RFREKSGVYF L YSGPREVF DGYIAPAMRF LGDTGIGGKS TWGAGLFEVE FHEMKIDAPG SEYSVTLSNA LPTKTPVLWR LLRKGGWSFG RR KPRMTFI AEGSIVKNDP GGMERLELGL SHEVYVYGLT FPLGVELPEG LE

UniProtKB: CRISPR system Cms protein Csm4

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Macromolecule #5: Csm5

MacromoleculeName: Csm5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 45.262145 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTERTLKVLS PLHIGTGNEL TPVDIYPREN IIHVLDTERL VNDLMNLGVE LNEILALLKN PPGDAYIWKG YIEEFHLDPS DYSIYTLKI HGKIGRKSMQ IKEFIKLNGR PYIPGSSLKG AIRTAVLYKA LKECGDARAV MRVVSKVNGD VARDIGRSED V LDYYMSFL ...String:
MTERTLKVLS PLHIGTGNEL TPVDIYPREN IIHVLDTERL VNDLMNLGVE LNEILALLKN PPGDAYIWKG YIEEFHLDPS DYSIYTLKI HGKIGRKSMQ IKEFIKLNGR PYIPGSSLKG AIRTAVLYKA LKECGDARAV MRVVSKVNGD VARDIGRSED V LDYYMSFL SRARIDRKRA DDLLEAIVFG MEPDRRSKIR YEPKRDPMKA LIVRDSKPVG RKHLAVYHVE VIGNPQPIPI WV EAIEPGA ATDVEIHVDT EALRLNADYF NGLLWECLKE RGEPGEVFED FLWEAVDEFY TAVMKYETIE VQKFGRYTSQ VRS FYASLE DHSGHVLRLG WGSGWLAMTI GLLLVEKGYK WENVRKKLGL GKKPGGSGFS REFPKTRRLA DGMPMGWVVL E

UniProtKB: CRISPR system Cms protein Csm5

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Macromolecule #6: RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*...

MacromoleculeName: RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP*UP*C)-3')
type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 7.707653 KDa
SequenceString:
GUGGAAAGUG GCCCGAAACC CUUC

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.875 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61924
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: COMMON LINE

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