+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21126 | |||||||||
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Title | Cryo-EM structure of Cascade-TniQ binary complex | |||||||||
Map data | Cascade-TniQ binary complex | |||||||||
Sample |
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Keywords | CRISPR-Cas system / Cascade- TniQ / IMMUNE SYSTEM | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Jia N / Patel DJ | |||||||||
Citation | Journal: Cell Res / Year: 2020 Title: Structure-function insights into the initial step of DNA integration by a CRISPR-Cas-Transposon complex. Authors: Ning Jia / Wei Xie / M Jason de la Cruz / Edward T Eng / Dinshaw J Patel / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21126.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-21126-v30.xml emd-21126.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21126_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_21126.png | 70.8 KB | ||
Filedesc metadata | emd-21126.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21126 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21126 | HTTPS FTP |
-Validation report
Summary document | emd_21126_validation.pdf.gz | 413.8 KB | Display | EMDB validaton report |
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Full document | emd_21126_full_validation.pdf.gz | 413.4 KB | Display | |
Data in XML | emd_21126_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | emd_21126_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21126 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21126 | HTTPS FTP |
-Related structure data
Related structure data | 6v9qMC 6v9pC 6vbwC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21126.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cascade-TniQ binary complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Cascade-TniQ binary complex
Entire | Name: Cascade-TniQ binary complex |
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Components |
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-Supramolecule #1: Cascade-TniQ binary complex
Supramolecule | Name: Cascade-TniQ binary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 400 KDa |
-Macromolecule #1: RNA (61-MER)
Macromolecule | Name: RNA (61-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 19.566543 KDa |
Sequence | String: CUGAUAACUU ACAGGACGCU UUGGCUUCAU UGCUUUUCAG GUGAACUGCC GAGUAGGUAG A |
-Macromolecule #2: Cas8
Macromolecule | Name: Cas8 / type: protein_or_peptide / ID: 2 / 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 |
-Macromolecule #3: TniQ family protein
Macromolecule | Name: TniQ family protein / type: protein_or_peptide / ID: 3 / 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 |
-Macromolecule #4: Type I-F CRISPR-associated protein Csy3
Macromolecule | Name: Type I-F CRISPR-associated protein Csy3 / type: protein_or_peptide / ID: 4 / 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 (E. coli) |
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 |
-Macromolecule #5: Type I-F CRISPR-associated endoribonuclease Cas6/Csy4
Macromolecule | Name: Type I-F CRISPR-associated endoribonuclease Cas6/Csy4 / type: protein_or_peptide / ID: 5 / 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 |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / 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
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 / Component - Formula: Tris / Details: 20 mM HEPES, pH 7.5, 150 mM NaCl, 2 mM DTT |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.16 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |