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- EMDB-20908: CryoEM structure of VcCascasde-TniQ complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20908
TitleCryoEM structure of VcCascasde-TniQ complex
Map dataComposite map of different focused refinement
Sample
  • Complex: protein complex 5
    • Protein or peptide: Cas6
    • Protein or peptide: Cas8/5
    • Protein or peptide: Cas7
    • Protein or peptide: TniQ
    • Other: crRNA
    • Protein or peptide: Cas8_HelicalBundle
  • Ligand: ZINC ION
KeywordsCRISPR CASCADE TniQ Transposition / Hydrolase-RNA complex
Biological speciesLachnospiraceae bacterium ND2006 (bacteria) / Vibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChang L / Li Z
CitationJournal: Cell Res / Year: 2020
Title: Cryo-EM structure of a type I-F CRISPR RNA guided surveillance complex bound to transposition protein TniQ.
Authors: Zhuang Li / Heng Zhang / Renjian Xiao / Leifu Chang /
History
DepositionNov 3, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseJan 29, 2020-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0215
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0215
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6uvn
  • Surface level: 0.0215
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20908.png

Downloads & links

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Map

FileDownload / File: emd_20908.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of different focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0215 / Movie #1: 0.0215
Minimum - Maximum-0.00093098026 - 0.25181502
Average (Standard dev.)0.0009809743 (±0.0060463212)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0010.2520.001

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Supplemental data

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Sample components

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Entire : protein complex 5

EntireName: protein complex 5
Components
  • Complex: protein complex 5
    • Protein or peptide: Cas6
    • Protein or peptide: Cas8/5
    • Protein or peptide: Cas7
    • Protein or peptide: TniQ
    • Other: crRNA
    • Protein or peptide: Cas8_HelicalBundle
  • Ligand: ZINC ION

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Supramolecule #1: protein complex 5

SupramoleculeName: protein complex 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)

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Macromolecule #1: Cas6

MacromoleculeName: Cas6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 25.136523 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SQDPNSSMVK WYYKTITFLP ELCNNESLAA KCLRVLHGFN YQYETRNIGV SFPLWCDATV GKKISFVSKN KIELDLLLK QHYFVQMEQL QYFHISNTVL VPEDCTYVSF RRCQSIDKLT AAGLARKIRR LEKRALSRGE QFDPSSFAQK E HTAIAHYH ...String:
MGSSHHHHHH SQDPNSSMVK WYYKTITFLP ELCNNESLAA KCLRVLHGFN YQYETRNIGV SFPLWCDATV GKKISFVSKN KIELDLLLK QHYFVQMEQL QYFHISNTVL VPEDCTYVSF RRCQSIDKLT AAGLARKIRR LEKRALSRGE QFDPSSFAQK E HTAIAHYH SLGESSKQTN RNFRLNIRML SEQPREGNSI FSSYGLSNSE NSFQPVPLI

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Macromolecule #2: Cas8/5

MacromoleculeName: Cas8/5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 72.29493 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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

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Macromolecule #3: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 40.185352 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MADLKLPTNL AYERSIDPSD VCFFVVWPDD RKTPLTYNSR TLLGQMEAAS LAYDVSGQPI KSATAEALAQ GNPHQVDFCH VPYGASHIE CSFSVSFSSE LRQPYKCNSS KVKQTLVQLV ELYETKIGWT ELATRYLMNI CNGKWLWKNT RKAYCWNIVL T PWPWNGEK ...String:
MADLKLPTNL AYERSIDPSD VCFFVVWPDD RKTPLTYNSR TLLGQMEAAS LAYDVSGQPI KSATAEALAQ GNPHQVDFCH VPYGASHIE CSFSVSFSSE LRQPYKCNSS KVKQTLVQLV ELYETKIGWT ELATRYLMNI CNGKWLWKNT RKAYCWNIVL T PWPWNGEK VGFEDIRTNY TSRQDFKNNK NWSAIVEMIK TAFSSTDGLA IFEVRATLHL PTNAMVRPSQ VFTEKESGSK SK SKTQNSR VFQSTTIDGE RSPILGAFKT GAAIATIDDW YPEATEPLRV GRFGVHREDV TCYRHPSTGK DFFSILQQAE HYI EVLSAN KTPAQETIND MHFLMANLIK GGMFQHKGD

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Macromolecule #4: TniQ

MacromoleculeName: TniQ / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 45.597867 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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

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Macromolecule #6: Cas8_HelicalBundle

MacromoleculeName: Cas8_HelicalBundle / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 8.358294 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)

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Macromolecule #5: crRNA

MacromoleculeName: crRNA / type: other / ID: 5 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 19.554586 KDa
SequenceString:
CUAAGAAAUU CACGGCGGGC UUGAUGUCCG CGUCUACCUG GUUCACUGCC GUGUAGGCA(DG) C
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 582000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

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