+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29459 | |||||||||
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Title | V. cholerae TniQ-Cascade complex with Type III-B crRNA | |||||||||
Map data | CAST Type I-F with Type III-B crRNA | |||||||||
Sample |
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Keywords | Type I-F CAST / DNA Transposition / CRISPR Transposon / ANTIVIRAL PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) / metagenome (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Chou CW / Finkelstein IJ / Hu K | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To be Published Title: V. cholerae TniQ-Cascade complex with Type III-B crRNA Authors: Chou CW / Finkelstein IJ / Hu K | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29459.map.gz | 290.7 MB | EMDB map data format | |
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Header (meta data) | emd-29459-v30.xml emd-29459.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29459_fsc.xml | 16.1 KB | Display | FSC data file |
Images | emd_29459.png | 115.1 KB | ||
Filedesc metadata | emd-29459.cif.gz | 6.7 KB | ||
Others | emd_29459_half_map_1.map.gz emd_29459_half_map_2.map.gz | 285 MB 285 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29459 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29459 | HTTPS FTP |
-Validation report
Summary document | emd_29459_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_29459_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_29459_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | emd_29459_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29459 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29459 | HTTPS FTP |
-Related structure data
Related structure data | 8fukMC 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_29459.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CAST Type I-F with Type III-B crRNA | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_29459_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_29459_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type I-F TniQ-Cascade with Type III-B crRNA
Entire | Name: Type I-F TniQ-Cascade with Type III-B crRNA |
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Components |
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-Supramolecule #1: Type I-F TniQ-Cascade with Type III-B crRNA
Supramolecule | Name: Type I-F TniQ-Cascade with Type III-B crRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 450 KDa |
-Macromolecule #1: Type III-B crRNA
Macromolecule | Name: Type III-B crRNA / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: metagenome (others) |
Molecular weight | Theoretical: 19.333586 KDa |
Sequence | String: CUUAGAAAAG UACAGCGCGG CUGAAAUCAU CAUUAAAGCG GUUCACUGCC GCACAGGCAG |
-Macromolecule #2: Cas7
Macromolecule | Name: Cas7 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 39.886031 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKLPTNLAYE RSIDPSDVCF FVVWPDDRKT PLTYNSRTLL GQMEAASLAY DVSGQPIKSA TAEALAQGNP HQVDFCHVPY GASHIECSF SVSFSSELRQ PYKCNSSKVK QTLVQLVELY ETKIGWTELA TRYLMNICNG KWLWKNTRKA YCWNIVLTPW P WNGEKVGF ...String: MKLPTNLAYE RSIDPSDVCF FVVWPDDRKT PLTYNSRTLL GQMEAASLAY DVSGQPIKSA TAEALAQGNP HQVDFCHVPY GASHIECSF SVSFSSELRQ PYKCNSSKVK QTLVQLVELY ETKIGWTELA TRYLMNICNG KWLWKNTRKA YCWNIVLTPW P WNGEKVGF EDIRTNYTSR QDFKNNKNWS AIVEMIKTAF SSTDGLAIFE VRATLHLPTN AMVRPSQVFT EKESGSKSKS KT QNSRVFQ STTIDGERSP ILGAFKTGAA IATIDDWYPE ATEPLRVGRF GVHREDVTCY RHPSTGKDFF SILQQAEHYI EVL SANKTP AQETINDMHF LMANLIKGGM FQHKGD UniProtKB: Cas7 |
-Macromolecule #3: CRISPR-associated protein Cas8
Macromolecule | Name: CRISPR-associated protein Cas8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 72.29493 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQTLKELIAS NPDDLTTELK RAFRPLTPHI AIDGNELDAL TILVNLTDKT DDQKDLLDRA KCKQKLRDEK WWASCINCVN YRQSHNPKF PDIRSEGVIR TQALGELPSF LLSSSKIPPY HWSYSHDSKY VNKSAFLTNE FCWDGEISCL GELLKDADHP L WNTLKKLG ...String: MQTLKELIAS NPDDLTTELK RAFRPLTPHI AIDGNELDAL TILVNLTDKT DDQKDLLDRA KCKQKLRDEK WWASCINCVN YRQSHNPKF PDIRSEGVIR TQALGELPSF LLSSSKIPPY HWSYSHDSKY VNKSAFLTNE FCWDGEISCL GELLKDADHP L WNTLKKLG CSQKTCKAMA KQLADITLTT INVTLAPNYL TQISLPDSDT SYISLSPVAS LSMQSHFHQR LQDENRHSAI TR FSRTTNM GVTAMTCGGA FRMLKSGAKF SSPPHHRLNS KRSWLTSEHV QSLKQYQRLN KSLIPENSRI ALRRKYKIEL QNM VRSWFA MQDHTLDSNI LIQHLNHDLS YLGATKRFAY DPAMTKLFTE LLKRELSNSI NNGEQHTNGS FLVLPNIRVC GATA LSSPV TVGIPSLTAF FGFVHAFERN INRTTSSFRV ESFAICVHQL HVEKRGLTAE FVEKGDGTIS APATRDDWQC DVVFS LILN TNFAQHIDQD TLVTSLPKRL ARGSAKIAID DFKHINSFST LETAIESLPI EAGRWLSLYA QSNNNLSDLL AAMTED HQL MASCVGYHLL EEPKDKPNSL RGYKHAIAEC IIGLINSITF SSETDPNTIF WSLKNYQNYL VVQPRSINDE TTDKSSL UniProtKB: Cas8 |
-Macromolecule #4: Cas6
Macromolecule | Name: Cas6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 23.13043 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKWYYKTITF LPELCNNESL AAKCLRVLHG FNYQYETRNI GVSFPLWCDA TVGKKISFVS KNKIELDLLL KQHYFVQMEQ LQYFHISNT VLVPEDCTYV SFRRCQSIDK LTAAGLARKI RRLEKRALSR GEQFDPSSFA QKEHTAIAHY HSLGESSKQT N RNFRLNIR ...String: MKWYYKTITF LPELCNNESL AAKCLRVLHG FNYQYETRNI GVSFPLWCDA TVGKKISFVS KNKIELDLLL KQHYFVQMEQ LQYFHISNT VLVPEDCTYV SFRRCQSIDK LTAAGLARKI RRLEKRALSR GEQFDPSSFA QKEHTAIAHY HSLGESSKQT N RNFRLNIR MLSEQPREGN SIFSSYGLSN SENSFQPVPL I UniProtKB: Cas6 |
-Macromolecule #5: TniQ
Macromolecule | Name: TniQ / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 45.597867 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MFLQRPKPYS DESLESFFIR VANKNGYGDV HRFLEATKRF LQDIDHNGYQ TFPTDITRIN PYSAKNSSSA RTASFLKLAQ LTFNEPPEL LGLAINRTNM KYSPSTSAVV RGAEVFPRSL LRTHSIPCCP LCLRENGYAS YLWHFQGYEY CHSHNVPLIT T CSCGKEFD ...String: MFLQRPKPYS DESLESFFIR VANKNGYGDV HRFLEATKRF LQDIDHNGYQ TFPTDITRIN PYSAKNSSSA RTASFLKLAQ LTFNEPPEL LGLAINRTNM KYSPSTSAVV RGAEVFPRSL LRTHSIPCCP LCLRENGYAS YLWHFQGYEY CHSHNVPLIT T CSCGKEFD YRVSGLKGIC CKCKEPITLT SRENGHEAAC TVSNWLAGHE SKPLPNLPKS YRWGLVHWWM GIKDSEFDHF SF VQFFSNW PRSFHSIIED EVEFNLEHAV VSTSELRLKD LLGRLFFGSI RLPERNLQHN IILGELLCYL ENRLWQDKGL IAN LKMNAL EATVMLNCSL DQIASMVEQR ILKPNRKSKP NSPLDVTDYL FHFGDIFCLW LAEFQSDEFN RSFYVSRW UniProtKB: TniQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 39.2 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 1235 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8fuk: |