+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27257 | |||||||||
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Title | Apo gRAMP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CRISPR / GRAMP / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RAMP superfamily protein Function and homology information | |||||||||
Biological species | Candidatus Scalindua brodae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Hu C / Nam KH / Schuler G / Ke A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2022 Title: Craspase is a CRISPR RNA-guided, RNA-activated protease. Authors: Chunyi Hu / Sam P B van Beljouw / Ki Hyun Nam / Gabriel Schuler / Fran Ding / Yanru Cui / Alicia Rodríguez-Molina / Anna C Haagsma / Menno Valk / Martin Pabst / Stan J J Brouns / Ailong Ke / Abstract: The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo-electron ...The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo-electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5' region of the guide RNA displaces a gating loop in gRAMP, which triggers an extensive conformational relay that allosterically aligns the protease catalytic dyad and opens an amino acid side-chain-binding pocket. We further define Csx30 as the endogenous protein substrate that is site-specifically proteolyzed by RNA-activated Craspase. This protease activity is switched off by target RNA cleavage by gRAMP and is not activated by RNA targets containing a matching protospacer flanking sequence. We thus conclude that Craspase is a target RNA-activated protease with self-regulatory capacity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27257.map.gz | 28.2 MB | EMDB map data format | |
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Header (meta data) | emd-27257-v30.xml emd-27257.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
Images | emd_27257.png | 114.7 KB | ||
Others | emd_27257_additional_1.map.gz emd_27257_half_map_1.map.gz emd_27257_half_map_2.map.gz | 56.5 MB 55.3 MB 55.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27257 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27257 | HTTPS FTP |
-Related structure data
Related structure data | 8d97MC 8d8nC 8d9eC 8d9fC 8d9gC 8d9hC 8d9iC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27257.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.284 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_27257_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27257_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27257_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : APO gRAMP
Entire | Name: APO gRAMP |
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Components |
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-Supramolecule #1: APO gRAMP
Supramolecule | Name: APO gRAMP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
-Macromolecule #1: RAMP superfamily protein
Macromolecule | Name: RAMP superfamily protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 184.351406 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MNITVELTFF EPYRLVEWFD WDARKKSHSA MRGQAFAQWT WKGKGRTAGK SFITGTLVRS AVIKAVEELL SLNNGKWEGV PCCNGSFQT DESKGKKPSF LRKRHTLQWQ ANNKNICDKE EACPFCILLG RFDNAGKVHE RNKDYDIHFS NFDLDHDLRL V DIASGRIL ...String: MNITVELTFF EPYRLVEWFD WDARKKSHSA MRGQAFAQWT WKGKGRTAGK SFITGTLVRS AVIKAVEELL SLNNGKWEGV PCCNGSFQT DESKGKKPSF LRKRHTLQWQ ANNKNICDKE EACPFCILLG RFDNAGKVHE RNKDYDIHFS NFDLDHDLRL V DIASGRIL NRVDFDTGKA KDYFRTWEAD YETYGTYTGR ITLRNEHAKK LLLASLGFVD KLCGALCRIE VIKSEDHNDE LR KQAEVIV EAFKQNDKLE KIRILADAIR TLRLHGEGVI EKDELPDGKE ERDKGHHLWD IKVQGTALRT KLKELWQSNK DIG WRKFTE MLGSNLYLIY KKETGGVSTR FRILGDTEYY SKAHDSEGSD LFIPVTPPEG IETKEWIIVG RLKAATPFYF GVQQ PSDSI PGKEKKSEDS LVINEHTSFN ILLDKENRYR IPRSALRGAL RRDLRTAFGS GCNVSLGGQI LCNCKVCIEM RRITL KDSV SDFSEPPEIR YRIAKNPGTA TVEDGSLFDI EVGPEGLTFP FVLRYRGHKF PEQLSSVIRY WEENDGKNGM AWLGGL DST GKGRFALKDI KIFEWDLNQK INEYIKERGM RGKEKELLEM GESSLPDGLI PYKFFEEREC LFPYKENLKP QWSEVQY TI EVGSPLLTAD TISALTEPGN RDAIAYKKRV YNDGNNAIEP EPRFAVKSET HRGIFRTAVG RRTGDLGKED HEDCTCDM C IIFGNEHESS KIRFEDLELI NGNEFEKLEK HIDHVAIDRF TGGALDKAKF DTYPLAGSPK KPLKLKGRFW IKKGFSGDH KLLITTALSD IRDGLYPLGS KGGVGYGWVA GISIDDNVPD DFKEMINKTY VHPGHQSPKQ DHKNKNIYYP HYFLDSGSKV YREKDIITH EEFTEELLSG KINCKLETLT PLIIPDTSDE NGLKLQGNKP GHKNYKFFNI NGELMIPGSE LRGMLRTHFE A LTKSCFAI FGETLSWRMN ADEKDYKIDS NSIRKMESQR NPKYRIPDEL QKELRNSGNG LFNRLYTSER RFWSDVSNKF EN SIDYKRE ILRCAGRPKN YKGGIIRQRK DSLMAEELKV HRLPLYDNFD IPDSAYKAND HCRKSATCST SRGCRERFTC GIK VRDKNR VFLNAANNNR QYLNNIKKSN HDLYLQYLKG EKKIRFNSKV ITGSERSPID VIAELNERGR QTGFIKLSGL NNSN KSQGN TGTTFNSGWD RFELNILLDD LETRPSKSDY PRPRLLFTKD QYEYNITKRC ERVFEIDKGN KTGYPVDDQI KKNYE DILD SYDGIKDQEV AERFDTFTRG SKLKVGDLVY FHIDGDNKID SLIPVRGKLD KALHPCTGLS DGLCPGCHLF GTTDYK GRV KFGFAKYENG PEWLITRGNN PERSLTLGVL ESPRPAFSIP DDESEIPGRK FYLHHNGWRI IRQKQLEIRE TVQPERN VT TEVMDKGNVF SFDVRFENLR EWELGLLLQS LDPGKNIAHK LGKGKPYGFG SVKIKIDSLH TFKIIKRVPQ SDIREYIN K GYQKLIEWSL PQWHVIPHID KLYKLLWVPF LNDSKLEPDV RYPVLNYTYK KLGDKDNLPY KTRVKGLTTP WSPWNPFQV |
-Macromolecule #2: RNA (42-MER)
Macromolecule | Name: RNA (42-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 13.295887 KDa |
Sequence | String: UUAAUGUCAC GGUACCCAAU UUUCUGCCCC GGACUCCACG GC |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21741 |