+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27261 | |||||||||
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Title | gRAMP-TPR-CHAT Non match PFS target RNA(Craspase) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CRISPR / GRAMP / RNA BINDING PROTEIN / Craspase / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | CHAT domain / CHAT domain / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RAMP superfamily protein / CHAT domain protein Function and homology information | |||||||||
Biological species | Candidatus Scalindua brodae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.57 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_27261.map.gz | 27.5 MB | EMDB map data format | |
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Header (meta data) | emd-27261-v30.xml emd-27261.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
Images | emd_27261.png | 124.3 KB | ||
Others | emd_27261_additional_1.map.gz emd_27261_half_map_1.map.gz emd_27261_half_map_2.map.gz | 27.8 MB 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27261 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27261 | HTTPS FTP |
-Related structure data
Related structure data | 8d9gMC 8d8nC 8d97C 8d9eC 8d9fC 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_27261.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_27261_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27261_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27261_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : gRAMP-TPR-CHAT with Non match PFS target RNA Craspase
Entire | Name: gRAMP-TPR-CHAT with Non match PFS target RNA Craspase |
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Components |
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-Supramolecule #1: gRAMP-TPR-CHAT with Non match PFS target RNA Craspase
Supramolecule | Name: gRAMP-TPR-CHAT with Non match PFS target RNA Craspase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
-Macromolecule #1: CHAT domain protein
Macromolecule | Name: CHAT domain 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: 78.403711 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: PTREDIDRKE AERLLDEAFN PRTKPVDRKK IINSALKILI GLYKEKKDDL TSASFISIAR AYYLVSITIL PKGTTIPEKK KEALRKGIE FIDRAINKFN GSILDSQRAF RIKSVLSIEF NRIDREKCDN IKLKNLLNEA VDKGCTDFDT YEWDIQIAIR L CELGVDME ...String: PTREDIDRKE AERLLDEAFN PRTKPVDRKK IINSALKILI GLYKEKKDDL TSASFISIAR AYYLVSITIL PKGTTIPEKK KEALRKGIE FIDRAINKFN GSILDSQRAF RIKSVLSIEF NRIDREKCDN IKLKNLLNEA VDKGCTDFDT YEWDIQIAIR L CELGVDME GHFDNLIKSN KANDLQKAKA YYFIKKDDHK AKEHMDKCTA SLKYTPCSHR LWDETVGFIE RLKGDSSTLW RD FAIKTYR SCRVQEKETG TLRLRWYWSR HRVLYDMAFL AVKEQADDEE PDVNVKQAKI KKLAEISDSL KSRFSLRLSD MEK MPKSDD ESNHEFKKFL DKCVTAYRSI YVINRKLLEL TQVPEGWVVV HFYLNKLEGM GNAIVFDKCA NSWQYKEFQY KELF EVFLT WQANYNLYKE NAAEHLVTLC KKIGETMPFL FCDNFIPNGK DVLFVPHDFL HRLPLHGSIE NKTNGKLFLE NHSCC YLPA WSFASEKEAS TSDEYVLLKN FDQGHFETLQ NNQIWGTQSV KDGASSDDLE NIRNNPRLLT ILCHGEANMS NPFRSM LKL ANGGITYLEI LNSVKGLKGS QVILGACETD LVPPLSDVMD EHYSVATALL LIGAAGVVGT MWKVRSNKTK SLIEWKL EN IEYKLNEWQK ETGGAAYKDH PPTFYRSIAF RSIGFPL |
-Macromolecule #2: RAMP superfamily protein
Macromolecule | Name: RAMP superfamily protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 147.151625 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 NFDLDHKQEK N DLRLVDIA ...String: MNITVELTFF EPYRLVEWFD WDARKKSHSA MRGQAFAQWT WKGKGRTAGK SFITGTLVRS AVIKAVEELL SLNNGKWEGV PCCNGSFQT DESKGKKPSF LRKRHTLQWQ ANNKNICDKE EACPFCILLG RFDNAGKVHE RNKDYDIHFS NFDLDHKQEK N DLRLVDIA SGRILNRVDF DTGKAKDYFR TWEADYETYG TYTGRITLRN EHAKKLLLAS LGFVDKLCGA LCRIEVIKDH ND ELRKQAE VIVEAFKQND KLEKIRILAD AIRTLRLHGE GVIEKDELPD GKEERDKGHH LWDIKVQGTA LRTKLKELWQ SNK DIGWRK FTEMLGSNLY LIYKKETGGV STRFRILGDT EYYSKAHDSE GSDLFIPVTP PEGIETKEWI IVGRLKAATP FYFG VQQPS DSIPGKEKKS EDSLVINEHT SFNILLDKEN RYRIPRSALR GALRRDLRTA FGSGCNVSLG GQILCNCKVC IEMRR ITLK DSVSDFSEPP EIRYRIAKNP GTATVEDGSL FDIEVGPEGL TFPFVLRYRG HKFPEQLSSV IRYWEENDGK NGMAWL GGL DSTGKGRFAL KDIKIFEWDL NQKINEYIKE RGMRGKEKEL LEMGESSLPD GLIPYKFFEE RECLFPYKEN LKPQWSE VQ YTIEVGSPLL TADTISALTE PGNRDAIAYK KRVYNDGNNA IEPEPRFAVK SETHRGIFRT AVGRRTGDLG KEDHEDCT C DMCIIFGNEH ESSKIRFEDL ELINGNEFEK LEKHIDHVAI DRFTGGALDK AKFDTYPLAG SPKKPLKLKG RFWIKKGFS GDHKLLITTA LSDIRDGLYP LGSKGGVGYG WVAGISIDDN VPDDFKEMIN KTNNDYVHPG HQSPKQDHKN KNIYYPHYFL DSGSKVYRE KDIITHEEFT EELLSGKINC KLETLTPLII PDTSDENGLK LQGNKPGHKN YKFFNINGEL MIPGSELRGM L RTHFEALT KSCFAIFGED STLSWASKTL GGKLDKALHP CTGLSDGLCP GCHLFGTTDY KGRVKFGFAK YENGPEWLIT RG NNPERSL TLGVLESPRP AFSIPDDESE IPGRKFYLHH NGWRIIRQKQ LEIRETVQPE RNVTTEVMDK GNVFSFDVRF ENL REWELG LLLQSLDPGK NIAHKLGKGK PYGFGSVKIK IDSLHTFKIN SNNDKIKRVP QSDIREYINK GYQKLIEWSG NNSI QKGNV LPQWHVIPHI DKLYKLLWVP FLNDSKLEPD VRYPVLNEES KGYIEGSDYT YKKLGDKDNL PYKTRVKGLT TPWSP WNPF QV |
-Macromolecule #3: RNA (36-MER)
Macromolecule | Name: RNA (36-MER) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 11.423787 KDa |
Sequence | String: GACUUAAUGU CACGGUACCC AAUUUUCUGC CCCGGA |
-Macromolecule #4: RNA (5'-R(P*UP*CP*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP...
Macromolecule | Name: RNA (5'-R(P*UP*CP*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*CP*GP*AP*U)-3') type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 7.466521 KDa |
Sequence | String: UCCGGGGCAG AAAAUUGGAC GAU |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / 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 TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 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: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / 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: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 340526 |