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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9708 | |||||||||
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Title | Cryo-EM structure of Csm effector complex | |||||||||
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Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
![]() | Huo Y / Li T / Wang N / Dong Q / Wang X / Jiang T | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 48.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.2 KB 16.2 KB | Display Display | ![]() |
Images | ![]() | 176 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 578.5 KB | Display | ![]() |
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Full document | ![]() | 578.1 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iqwMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : ToCsm effector complex
Entire | Name: ToCsm effector complex |
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Components |
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-Supramolecule #1: ToCsm effector complex
Supramolecule | Name: ToCsm effector complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Csm1
Macromolecule | Name: Csm1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 88.131898 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Csm2
Macromolecule | Name: Csm2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 22.410691 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: Csm3
Macromolecule | Name: Csm3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 32.721936 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #4: Csm4
Macromolecule | Name: Csm4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 32.345061 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #5: Csm5
Macromolecule | Name: Csm5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.262145 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #6: RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*...
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 7.707653 KDa |
Sequence | String: GUGGAAAGUG GCCCGAAACC CUUC |
-Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | 3D array |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.875 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61924 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: COMMON LINE |