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- EMDB-29459: V. cholerae TniQ-Cascade complex with Type III-B crRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-29459
TitleV. cholerae TniQ-Cascade complex with Type III-B crRNA
Map dataCAST Type I-F with Type III-B crRNA
Sample
  • Complex: Type I-F TniQ-Cascade with Type III-B crRNA
    • RNA: Type III-B crRNA
    • Protein or peptide: Cas7
    • Protein or peptide: CRISPR-associated protein Cas8
    • Protein or peptide: Cas6
    • Protein or peptide: TniQ
KeywordsType I-F CAST / DNA Transposition / CRISPR Transposon / ANTIVIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity
Similarity search - Function
TniQ / TniQ / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3)
Similarity search - Domain/homology
Cas6 / CRISPR-associated protein Cas8 / Cas7 / TniQ
Similarity search - Component
Biological speciesVibrio cholerae (bacteria) / metagenome (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsChou CW / Finkelstein IJ / Hu K
Funding support United States, 2 items
OrganizationGrant numberCountry
Welch Foundation2674221058 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2616141758 United States
CitationJournal: To be Published
Title: V. cholerae TniQ-Cascade complex with Type III-B crRNA
Authors: Chou CW / Finkelstein IJ / Hu K
History
DepositionJan 17, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29459.png

Downloads & links

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Map

FileDownload / File: emd_29459.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCAST Type I-F with Type III-B crRNA
Voxel sizeX=Y=Z: 0.94 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.6848763 - 1.2250837
Average (Standard dev.)-0.00023112624 (±0.02605502)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 406.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_29459_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_29459_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type I-F TniQ-Cascade with Type III-B crRNA

EntireName: Type I-F TniQ-Cascade with Type III-B crRNA
Components
  • Complex: Type I-F TniQ-Cascade with Type III-B crRNA
    • RNA: Type III-B crRNA
    • Protein or peptide: Cas7
    • Protein or peptide: CRISPR-associated protein Cas8
    • Protein or peptide: Cas6
    • Protein or peptide: TniQ

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Supramolecule #1: Type I-F TniQ-Cascade with Type III-B crRNA

SupramoleculeName: Type I-F TniQ-Cascade with Type III-B crRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: Type III-B crRNA

MacromoleculeName: Type III-B crRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 19.333586 KDa
SequenceString:
CUUAGAAAAG UACAGCGCGG CUGAAAUCAU CAUUAAAGCG GUUCACUGCC GCACAGGCAG

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Macromolecule #2: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 39.886031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #3: CRISPR-associated protein Cas8

MacromoleculeName: CRISPR-associated protein Cas8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 72.29493 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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: CRISPR-associated protein Cas8

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Macromolecule #4: Cas6

MacromoleculeName: Cas6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 23.13043 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #5: TniQ

MacromoleculeName: TniQ / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 45.597867 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 39.2 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 1235 / Average electron dose: 40.0 e/Å2

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6pig

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 50 / Avg.num./class: 10000
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 67000
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8fuk:
V. cholerae TniQ-Cascade complex with Type III-B crRNA

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