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Yorodumi- EMDB-33677: CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33677 | |||||||||
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Title | CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA complex bound to non-self RNA target | |||||||||
Map data | ||||||||||
Sample |
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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: 2.54 Å | |||||||||
Authors | Zhang JT / Cui N / Huang HD / Jia N | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the non-self RNA-activated protease activity of the type III-E CRISPR nuclease-protease Craspase Authors: Cui N / Zhang JT / Li Z / Liu XY / Wang C / Huang H / Jia N | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33677.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-33677-v30.xml emd-33677.xml | 18 KB 18 KB | Display Display | EMDB header |
Images | emd_33677.png | 75.3 KB | ||
Masks | emd_33677_msk_1.map | 64 MB | Mask map | |
Others | emd_33677_half_map_1.map.gz emd_33677_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33677 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33677 | HTTPS FTP |
-Related structure data
Related structure data | 7y81MC 7y80C 7y82C 7y83C 7y84C 7y85C 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_33677.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33677_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33677_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33677_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type III-E CRISPR gRAMP-crRNA binary complex
Entire | Name: Type III-E CRISPR gRAMP-crRNA binary complex |
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Components |
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-Supramolecule #1: Type III-E CRISPR gRAMP-crRNA binary complex
Supramolecule | Name: Type III-E CRISPR gRAMP-crRNA binary complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
-Supramolecule #2: gRAMP
Supramolecule | Name: gRAMP / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
-Supramolecule #3: crRNA
Supramolecule | Name: crRNA / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Supramolecule #4: Non-self RNA target
Supramolecule | Name: Non-self RNA target / type: complex / Chimera: Yes / ID: 4 / Parent: 1 / Macromolecule list: #3 |
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-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: 198.652688 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MHHHHHHKSN DMNITVELTF FEPYRLVEWF DWDARKKSHS AMRGQAFAQW TWKGKGRTAG KSFITGTLVR SAVIKAVEEL LSLNNGKWE GVPCCNGSFQ TDESKGKKPS FLRKRHTLQW QANNKNICDK EEACPFCILL GRFDNAGKVH ERNKDYDIHF S NFDLDHKQ ...String: MHHHHHHKSN DMNITVELTF FEPYRLVEWF DWDARKKSHS AMRGQAFAQW TWKGKGRTAG KSFITGTLVR SAVIKAVEEL LSLNNGKWE GVPCCNGSFQ TDESKGKKPS FLRKRHTLQW QANNKNICDK EEACPFCILL GRFDNAGKVH ERNKDYDIHF S NFDLDHKQ EKNDLRLVDI ASGRILNRVD FDTGKAKDYF RTWEADYETY GTYTGRITLR NEHAKKLLLA SLGFVDKLCG AL CRIEVIK KSESPLPSDT KEQSYTKDDT VEVLSEDHND ELRKQAEVIV EAFKQNDKLE KIRILADAIR TLRLHGEGVI EKD ELPDGK EERDKGHHLW DIKVQGTALR TKLKELWQSN KDIGWRKFTE MLGSNLYLIY KKETGGVSTR FRILGDTEYY SKAH DSEGS DLFIPVTPPE GIETKEWIIV GRLKAATPFY FGVQQPSDSI PGKEKKSEDS LVINEHTSFN ILLDKENRYR IPRSA LRGA LRRDLRTAFG SGCNVSLGGQ ILCNCKVCIE MRRITLKDSV SDFSEPPEIR YRIAKNPGTA TVEDGSLFDI EVGPEG LTF PFVLRYRGHK FPEQLSSVIR YWEENDGKNG MAWLGGLDST GKGRFALKDI KIFEWDLNQK INEYIKERGM RGKEKEL LE MGESSLPDGL IPYKFFEERE CLFPYKENLK PQWSEVQYTI EVGSPLLTAD TISALTEPGN RDAIAYKKRV YNDGNNAI E PEPRFAVKSE THRGIFRTAV GRRTGDLGKE DHEDCTCDMC IIFGNEHESS KIRFEDLELI NGNEFEKLEK HIDHVAIDR FTGGALDKAK FDTYPLAGSP KKPLKLKGRF WIKKGFSGDH KLLITTALSD IRDGLYPLGS KGGVGYGWVA GISIDDNVPD DFKEMINKT EMPLPEEVEE SNNGPINNDY VHPGHQSPKQ DHKNKNIYYP HYFLDSGSKV YREKDIITHE EFTEELLSGK I NCKLETLT PLIIPDTSDE NGLKLQGNKP GHKNYKFFNI NGELMIPGSE LRGMLRTHFE ALTKSCFAIF GEDSTLSWRM NA DEKDYKI DSNSIRKMES QRNPKYRIPD ELQKELRNSG NGLFNRLYTS ERRFWSDVSN KFENSIDYKR EILRCAGRPK NYK GGIIRQ RKDSLMAEEL KVHRLPLYDN FDIPDSAYKA NDHCRKSATC STSRGCRERF TCGIKVRDKN RVFLNAANNN RQYL NNIKK SNHDLYLQYL KGEKKIRFNS KVITGSERSP IDVIAELNER GRQTGFIKLS GLNNSNKSQG NTGTTFNSGW DRFEL NILL DDLETRPSKS DYPRPRLLFT KDQYEYNITK RCERVFEIDK GNKTGYPVDD QIKKNYEDIL DSYDGIKDQE VAERFD TFT RGSKLKVGDL VYFHIDGDNK IDSLIPVRIS RKCASKTLGG KLDKALHPCT GLSDGLCPGC HLFGTTDYKG RVKFGFA KY ENGPEWLITR GNNPERSLTL GVLESPRPAF SIPDDESEIP GRKFYLHHNG WRIIRQKQLE IRETVQPERN VTTEVMDK G NVFSFDVRFE NLREWELGLL LQSLDPGKNI AHKLGKGKPY GFGSVKIKID SLHTFKINSN NDKIKRVPQS DIREYINKG YQKLIEWSGN NSIQKGNVLP QWHVIPHIDK LYKLLWVPFL NDSKLEPDVR YPVLNEESKG YIEGSDYTYK KLGDKDNLPY KTRVKGLTT PWSPWNPFQV IAEHEEQEVN VTGSRPSVTD KIERDGKMV |
-Macromolecule #2: crRNA
Macromolecule | Name: crRNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 35.43209 KDa |
Sequence | String: GUUAUGAAAC AAGAGAAGGA CUUAAUGUCA CGGUACCCAA UUUUCUGCCC CGGACUCCAC GGCUGUUACU AGAGGUUAUG AAACAAGAG AAGGACUUAA UGUCACGGUA C |
-Macromolecule #3: Non-self RNA target
Macromolecule | Name: Non-self RNA target / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 18.097797 KDa |
Sequence | String: CUCUAGUAAC AGCCGUGGAG UCCGGGGCAG AAAAUUGGCA UGGCACUGUA AUUCAG |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: RANDOM ASSIGNMENT |
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Final angle assignment | Type: RANDOM ASSIGNMENT |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 444936 |