+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33695 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the Cas7-11-Csx29-guide RNA complex | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | CRISPR / RNase / RNA BINDING PROTEIN-RNA COMPLEX | |||||||||
Function / homology | CHAT domain / CHAT domain / : / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / CRISPR-associated RAMP family protein / CHAT domain-containing protein Function and homology information | |||||||||
Biological species | Desulfonema ishimotonii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||
Authors | Kato K / Okazaki S / Ishikawa J / Isayama Y / Nishizawa T / Nishimasu H | |||||||||
Funding support | Japan, 1 items
| |||||||||
Citation | Journal: Science / Year: 2022 Title: RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease. Authors: Kazuki Kato / Sae Okazaki / Cian Schmitt-Ulms / Kaiyi Jiang / Wenyuan Zhou / Junichiro Ishikawa / Yukari Isayama / Shungo Adachi / Tomohiro Nishizawa / Kira S Makarova / Eugene V Koonin / ...Authors: Kazuki Kato / Sae Okazaki / Cian Schmitt-Ulms / Kaiyi Jiang / Wenyuan Zhou / Junichiro Ishikawa / Yukari Isayama / Shungo Adachi / Tomohiro Nishizawa / Kira S Makarova / Eugene V Koonin / Omar O Abudayyeh / Jonathan S Gootenberg / Hiroshi Nishimasu / Abstract: The type III-E CRISPR-Cas7-11 effector binds a CRISPR RNA (crRNA) and the putative protease Csx29 and catalyzes crRNA-guided RNA cleavage. We report cryo-electron microscopy structures of the Cas7-11- ...The type III-E CRISPR-Cas7-11 effector binds a CRISPR RNA (crRNA) and the putative protease Csx29 and catalyzes crRNA-guided RNA cleavage. We report cryo-electron microscopy structures of the Cas7-11-crRNA-Csx29 complex with and without target RNA (tgRNA), and demonstrate that tgRNA binding induces conformational changes in Csx29. Biochemical experiments revealed tgRNA-dependent cleavage of the accessory protein Csx30 by Csx29. Reconstitution of the system in bacteria showed that Csx30 cleavage yields toxic protein fragments that cause growth arrest, which is regulated by Csx31. Csx30 binds Csx31 and the associated sigma factor RpoE (RNA polymerase, extracytoplasmic E), suggesting that Csx30-mediated RpoE inhibition modulates the cellular response to infection. We engineered the Cas7-11-Csx29-Csx30 system for programmable RNA sensing in mammalian cells. Overall, the Cas7-11-Csx29 effector is an RNA-dependent nuclease-protease. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_33695.map.gz | 168 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-33695-v30.xml emd-33695.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_33695.png | 75.6 KB | ||
Masks | emd_33695_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-33695.cif.gz | 7.2 KB | ||
Others | emd_33695_half_map_1.map.gz emd_33695_half_map_2.map.gz | 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33695 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33695 | HTTPS FTP |
-Validation report
Summary document | emd_33695_validation.pdf.gz | 901.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_33695_full_validation.pdf.gz | 901.2 KB | Display | |
Data in XML | emd_33695_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_33695_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33695 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33695 | HTTPS FTP |
-Related structure data
Related structure data | 7y9xMC 7y9yC 8gs2C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_33695.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_33695_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_33695_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_33695_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Cas7-11 in complex with a crRNA and its target RNA
Entire | Name: Cas7-11 in complex with a crRNA and its target RNA |
---|---|
Components |
|
-Supramolecule #1: Cas7-11 in complex with a crRNA and its target RNA
Supramolecule | Name: Cas7-11 in complex with a crRNA and its target RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Source (natural) | Organism: Desulfonema ishimotonii (bacteria) |
-Supramolecule #2: Cas7-11, Csx29
Supramolecule | Name: Cas7-11, Csx29 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Desulfonema ishimotonii (bacteria) |
-Supramolecule #3: RNA
Supramolecule | Name: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
---|
-Macromolecule #1: CHAT domain-containing protein
Macromolecule | Name: CHAT domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Desulfonema ishimotonii (bacteria) |
Molecular weight | Theoretical: 88.311875 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSNPIRDIQD RLKTAKFDNK DDMMNLASSL YKYEKQLMDS SEATLCQQGL SNRPNSFSQL SQFRDSDIQS KAGGQTGKFW QNEYEACKN FQTHKERRET LEQIIRFLQN GAEEKDADDL LLKTLARAYF HRGLLYRPKG FSVPARKVEA MKKAIAYCEI I LDKNEEES ...String: MSNPIRDIQD RLKTAKFDNK DDMMNLASSL YKYEKQLMDS SEATLCQQGL SNRPNSFSQL SQFRDSDIQS KAGGQTGKFW QNEYEACKN FQTHKERRET LEQIIRFLQN GAEEKDADDL LLKTLARAYF HRGLLYRPKG FSVPARKVEA MKKAIAYCEI I LDKNEEES EALRIWLYAA MELRRCGEEY PENFAEKLFY LANDGFISEL YDIRLFLEYT EREEDNNFLD MILQENQDRE RL FELCLYK ARACFHLNQL NDVRIYGESA IDNAPGAFAD PFWDELVEFI RMLRNKKSEL WKEIAIKAWD KCREKEMKVG NNI YLSWYW ARQRELYDLA FMAQDGIEKK TRIADSLKSR TTLRIQELNE LRKDAHRKQN RRLEDKLDRI IEQENEARDG AYLR RNPPC FTGGKREEIP FARLPQNWIA VHFYLNELES HEGGKGGHAL IYDPQKAEKD QWQDKSFDYK ELHRKFLEWQ ENYIL NEEG SADFLVTLCR EIEKAMPFLF KSEVIPEDRP VLWIPHGFLH RLPLHAAMKS GNNSNIEIFW ERHASRYLPA WHLFDP APY SREESSTLLK NFEEYDFQNL ENGEIEVYAP SSPKKVKEAI RENPAILLLL CHGEADMTNP FRSCLKLKNK DMTIFDL LT VEDVRLSGSR ILLGACESDM VPPLEFSVDE HLSVSGAFLS HKAGEIVAGL WTVDSEKVDE CYSYLVEEKD FLRNLQEW Q MAETENFRSE NDSSLFYKIA PFRIIGFPAE UniProtKB: CHAT domain-containing protein |
-Macromolecule #2: CRISPR-associated RAMP family protein
Macromolecule | Name: CRISPR-associated RAMP family protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Desulfonema ishimotonii (bacteria) |
Molecular weight | Theoretical: 185.609875 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTTTMKISIE FLEPFRMTKW QESTRRNKNN KEFVRGQAFA RWHRNKKDNT KGRPYITGTL LRSAVIRSAE NLLTLSDGKI SEKTCCPGK FDTEDKDRLL QLRQRSTLRW TDKNPCPDNA ETYCPFCELL GRSGNDGKKA EKKDWRFRIH FGNLSLPGKP D FDGPKAIG ...String: MTTTMKISIE FLEPFRMTKW QESTRRNKNN KEFVRGQAFA RWHRNKKDNT KGRPYITGTL LRSAVIRSAE NLLTLSDGKI SEKTCCPGK FDTEDKDRLL QLRQRSTLRW TDKNPCPDNA ETYCPFCELL GRSGNDGKKA EKKDWRFRIH FGNLSLPGKP D FDGPKAIG SQRVLNRVDF KSGKAHDFFK AYEVDHTRFP RFEGEITIDN KVSAEARKLL CDSLKFTDRL CGALCVIRFD EY TPAADSG KQTENVQAEP NANLAEKTAE QIISILDDNK KTEYTRLLAD AIRSLRRSSK LVAGLPKDHD GKDDHYLWDI GKK KKDENS VTIRQILTTS ADTKELKNAG KWREFCEKLG EALYLKSKDM SGGLKITRRI LGDAEFHGKP DRLEKSRSVS IGSV LKETV VCGELVAKTP FFFGAIDEDA KQTALQVLLT PDNKYRLPRS AVRGILRRDL QTYFDSPCNA ELGGRPCMCK TCRIM RGIT VMDARSEYNA PPEIRHRTRI NPFTGTVAEG ALFNMEVAPE GIVFPFQLRY RGSEDGLPDA LKTVLKWWAE GQAFMS GAA STGKGRFRME NAKYETLDLS DENQRNDYLK NWGWRDEKGL EELKKRLNSG LPEPGNYRDP KWHEINVSIE MASPFIN GD PIRAAVDKRG TAVVTFVKYK AEGEEAKPVC AYKAESFRGV IRSAVARIHM EDGVPLTELT HSDCECLLCQ IFGSEYEA G KIRFEDLVFE SDPEPVTFDH VAIDRFTGGA AAKKKFDDSP LPGSPARPLM LKGSFWIRRD VLEDEEYCKA LGKALADVN NGLYPLGGKS AIGYGQVKSL GIKGDDKRIS RLMNPAFDET DVAVPEKPKT DAEVRIEAEK VYYPHYFVEP HKKVEREEKP CGHQKFHEG RLTGKIRCKL ITKTPLIVPD TSNDDFFRPA DKEARKEKDE YHKSYAFFRL HKQIMIPGSE LRGMVSSVYE T VTNSCFRI FDETKRLSWR MDADHQNVLQ DFLPGRVTAD GKHIQKFSET ARVPFYDKTQ KHFDILDEQE IAGEKPVRMW VK RFIKRLS LVDPAKHPQK KQDNKWKRRK EGIATFIEQK NGSYYFNVVT NNGCTSFHLW HKPDNFDQEK LEGIQNGEKL DCW VRDSRY QKAFQEIPEN DPDGWECKEG YLHVVGPSKV EFSDKKGDVI NNFQGTLPSV PNDWKTIRTN DFKNRKRKNE PVFC CEDDK GNYYTMAKYC ETFFFDLKEN EEYEIPEKAR IKYKELLRVY NNNPQAVPES VFQSRVAREN VEKLKSGDLV YFKHN EKYV EDIVPVRISR TVDDRMIGKR MSADLRPCHG DWVEDGDLSA LNAYPEKRLL LRHPKGLCPA CRLFGTGSYK GRVRFG FAS LENDPEWLIP GKNPGDPFHG GPVMLSLLER PRPTWSIPGS DNKFKVPGRK FYVHHHAWKT IKDGNHPTTG KAIEQSP NN RTVEALAGGN SFSFEIAFEN LKEWELGLLI HSLQLEKGLA HKLGMAKSMG FGSVEIDVES VRLRKDWKQW RNGNSEIP N WLGKGFAKLK EWFRDELDFI ENLKKLLWFP EGDQAPRVCY PMLRKKDDPN GNSGYEELKD GEFKKEDRQK KLTTPWTPW ASSGLVPRGS HHHHHHH UniProtKB: CRISPR-associated RAMP family protein |
-Macromolecule #3: crRNA
Macromolecule | Name: crRNA / type: rna / ID: 3 / Number of copies: 1 |
---|---|
Source (natural) | Organism: Desulfonema ishimotonii (bacteria) |
Molecular weight | Theoretical: 12.134133 KDa |
Sequence | String: UUGAUGUCAC GGAACCUUUG UUGUCUUCGA CAUGGGUA |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 76.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 691666 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |