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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9654 | |||||||||
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Title | Cryo-EM structure of type III-A Csm-NTR complex | |||||||||
![]() | Cryo-EM structure of type III-A Csm-NTR complex | |||||||||
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![]() | Csm complex / Type III-A / CRISPR-Cas system / RNA BINDING PROTEIN | |||||||||
Function / homology | ![]() exonuclease activity / transferase activity / endonuclease activity / defense response to virus / RNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
![]() | You L / Ma J | |||||||||
![]() | ![]() Title: Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference. Authors: Lilan You / Jun Ma / Jiuyu Wang / Daria Artamonova / Min Wang / Liang Liu / Hua Xiang / Konstantin Severinov / Xinzheng Zhang / Yanli Wang / ![]() ![]() Abstract: Csm, a type III-A CRISPR-Cas interference complex, is a CRISPR RNA (crRNA)-guided RNase that also possesses target RNA-dependent DNase and cyclic oligoadenylate (cOA) synthetase activities. However, ...Csm, a type III-A CRISPR-Cas interference complex, is a CRISPR RNA (crRNA)-guided RNase that also possesses target RNA-dependent DNase and cyclic oligoadenylate (cOA) synthetase activities. However, the structural features allowing target RNA-binding-dependent activation of DNA cleavage and cOA generation remain unknown. Here, we report the structure of Csm in complex with crRNA together with structures of cognate or non-cognate target RNA bound Csm complexes. We show that depending on complementarity with the 5' tag of crRNA, the 3' anti-tag region of target RNA binds at two distinct sites of the Csm complex. Importantly, the interaction between the non-complementary anti-tag region of cognate target RNA and Csm1 induces a conformational change at the Csm1 subunit that allosterically activates DNA cleavage and cOA generation. Together, our structural studies provide crucial insights into the mechanistic processes required for crRNA-meditated sequence-specific RNA cleavage, RNA target-dependent non-specific DNA cleavage, and cOA generation. | |||||||||
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 | ![]() | 28.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
Images | ![]() | 64.1 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Others | ![]() | 28.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iflMC ![]() 9653C ![]() 9655C ![]() 9656C ![]() 9657C ![]() 9658C ![]() 9659C ![]() 9660C ![]() 6ifkC ![]() 6ifnC ![]() 6ifrC ![]() 6ifuC ![]() 6ifyC ![]() 6ifzC ![]() 6ig0C 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
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Annotation | Cryo-EM structure of type III-A Csm-NTR complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Additional map: Cryo-EM structure of type III-A Csm-NTR complex,subunit Csm1
File | emd_9654_additional.map | ||||||||||||
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Annotation | Cryo-EM structure of type III-A Csm-NTR complex,subunit Csm1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Csm-CTR1 complex, AMPPNP bound
Entire | Name: Csm-CTR1 complex, AMPPNP bound |
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Components |
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-Supramolecule #1: Csm-CTR1 complex, AMPPNP bound
Supramolecule | Name: Csm-CTR1 complex, AMPPNP bound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: type III-A CRISPR-Cas interference complex |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 87 KDa |
-Supramolecule #2: Csm1
Supramolecule | Name: Csm1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: type III-A CRISPR-Cas interference complex subunit Csm1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Type III-A CRISPR-associated protein Csm1
Macromolecule | Name: Type III-A CRISPR-associated protein Csm1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 86.976734 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKKEKIDLFY GALLHNIGKV IQRATGERKK HALVGADWFD EIADNQVISD QIRYHMANYQ SDKLGNDHLA YITYIADNIA SGVDRRQSN EESDEDTSAK IWDTYTNQAD IFNVFGAQTD KRYFKPTVLN LKSKPNFASA TYEPFSKGDY AAIATRIKNE L AEFEFNQV ...String: MKKEKIDLFY GALLHNIGKV IQRATGERKK HALVGADWFD EIADNQVISD QIRYHMANYQ SDKLGNDHLA YITYIADNIA SGVDRRQSN EESDEDTSAK IWDTYTNQAD IFNVFGAQTD KRYFKPTVLN LKSKPNFASA TYEPFSKGDY AAIATRIKNE L AEFEFNQV QIDSLLNLFE ATLSFVPSST NTKEIADISL ADHSRLTAAF ALAIYDYLED KGRHNYKEDL FTKVSAFYEE EA FLLASFD LSGIQDFIYN INIATNGAAK QLKARSLYLD FMSEYIADSL LDKLGLNRAN MLYVGGGHAY FVLANTEKTV ETL VQFEKD FNQFLLANFQ TRLYVAFGWG SFAAKDIMSE LNSPESYRQV YQKASRMISK KKISRYDYQT LMLLNRGGKS SERE CEICH SVENLVSYHD QKVCDICRGL YQFSKEIAHD HFIITENEGL PIGPNACLKG VAFEKLSQEA FSRVYVKNDY KAGTV KATH VFVGDYQCDE IYNYAALSKN ENGLGIKRLA VVRLDVDDLG AAFMAGFSQQ GNGQYSTLSR SATFSRSMSL FFKVYI NQF ASDKKLSIIY AGGDDVFAIG SWQDIIAFTV ELRENFIKWT NGKLTLSAGI GLFADKTPIS LMAHQTGELE EAAKGNE KD SISLFSSDYT FKFDRFITNV YDDKLEQIRY FFNHQDERGK NFIYKLIELL RNHDRMNMAR LAYYLTRLEE LTRETDRD K FKTFKNLFYS WYTNKNDKDR KEAELALLLY IYEIRKD UniProtKB: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) |
-Macromolecule #2: Type III-A CRISPR-associated protein Csm2
Macromolecule | Name: Type III-A CRISPR-associated protein Csm2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.848145 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTILTDENYV DIAEKAILKL ERNTRNRKNP DAFFLTTSKL RNLLSLTSTL FDESKVKEYD ALLDRIAYLR VQFVYQAGRE IAVKDLIEK AQILEALKEI KDRETLQRFC RYMEALVAYF KFYGGKD UniProtKB: CRISPR system Cms protein Csm2 |
-Macromolecule #3: Type III-A CRISPR-associated RAMP protein Csm3
Macromolecule | Name: Type III-A CRISPR-associated RAMP protein Csm3 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.584855 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTFAKIKFSA QIRLETGLHI GGSDAFAAIG AINSPVIKDP ITNLPIIPGS SLKGKMRTLL AKVYNEKVAE KPSDDSDILS RLFGNSKDK RFKMGRLIFR DAFLSNADEL DSLGVRSYTE VKFENTIDRI TAEANPRQIE RAIRNSTFDF ELIYEITDEN E NQVEEDFK ...String: MTFAKIKFSA QIRLETGLHI GGSDAFAAIG AINSPVIKDP ITNLPIIPGS SLKGKMRTLL AKVYNEKVAE KPSDDSDILS RLFGNSKDK RFKMGRLIFR DAFLSNADEL DSLGVRSYTE VKFENTIDRI TAEANPRQIE RAIRNSTFDF ELIYEITDEN E NQVEEDFK VIRDGLKLLE LDYLGGSGSR GYGKVAFENL KATTVFGNYD VKTLNELLTA EV UniProtKB: CRISPR system Cms endoribonuclease Csm3 |
-Macromolecule #4: Type III-A CRISPR-associated RAMP protein Csm4
Macromolecule | Name: Type III-A CRISPR-associated RAMP protein Csm4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.828984 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTYKLYIMTF QNAHFGSGTL DSSKLTFSAD RIFSALVLEA LKMGKLDAFL AEANQDKFTL TDAFPFQFGP FLPKPIGYPK HDQIDQSVD VKEVRRQAKL SKKLQFLALE NVDDYLNGEL FENEEHAVID TVTKNQPHKD DNLYQVATTR FSNDTSLYVI A NESDLLNE ...String: MTYKLYIMTF QNAHFGSGTL DSSKLTFSAD RIFSALVLEA LKMGKLDAFL AEANQDKFTL TDAFPFQFGP FLPKPIGYPK HDQIDQSVD VKEVRRQAKL SKKLQFLALE NVDDYLNGEL FENEEHAVID TVTKNQPHKD DNLYQVATTR FSNDTSLYVI A NESDLLNE LMSSLQYSGL GGKRSSGFGR FELDIQNIPL ELSDRLTKNH SDKVMSLTTA LPVDADLEEA MEDGHYLLTK SS GFAFSHA TNENYRKQDL YKFASGSTFS KTFEGQIVDV RPLDFPHAVL NYAKPLFFKL EV UniProtKB: CRISPR system Cms protein Csm4 |
-Macromolecule #5: Type III-A CRISPR-associated RAMP protein Csm5
Macromolecule | Name: Type III-A CRISPR-associated RAMP protein Csm5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 41.102113 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKNDYRTFKL SLLTLAPIHI GNGEKYTSRE FIYENKKFYF PDMGKFYNKM VEKRLAEKFE AFLIQTRPNA RNNRLISFLN DNRIAERSF GGYSISETGL ESDKNPNSAG AINEVNKFIR DAFGNPYIPG SSLKGAIRTI LMNTTPKWNN ENAVNDFGRF P KENKNLIP ...String: MKNDYRTFKL SLLTLAPIHI GNGEKYTSRE FIYENKKFYF PDMGKFYNKM VEKRLAEKFE AFLIQTRPNA RNNRLISFLN DNRIAERSF GGYSISETGL ESDKNPNSAG AINEVNKFIR DAFGNPYIPG SSLKGAIRTI LMNTTPKWNN ENAVNDFGRF P KENKNLIP WGPKKGKEYD DLFNAIRVSD SKPFDNKSLI LVQKWDYSAK TNKAKPLPLY RESISPLTKI EFEITTTTDE AG RLIEELG KRAQAFYKDY KAFFLSEFPD DKIQANLQYP IYLGAGSGAW TKTLFKQADG ILQRRYSRMK TKMVKKGVLK LTK APLKTV KIPSGNHSLV KNHESFYEMG KANFMIKEID K UniProtKB: CRISPR system Cms protein Csm5 |
-Macromolecule #6: crRNA
Macromolecule | Name: crRNA / type: rna / ID: 6 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.39277 KDa |
Sequence | String: ACGGAAACGC UUUCUAGCUC GCUAUAAUUA CCCAUU |
-Macromolecule #7: NTR
Macromolecule | Name: NTR / type: rna / ID: 7 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.937306 KDa |
Sequence | String: GGUAGGAAUG GGUAAUUAUA GCGAGCUAGA AAGCGUUUCC GUC |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
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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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133127 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |