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- EMDB-20910: Cryo-EM structure of VcCascade-TniQ supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-20910
TitleCryo-EM structure of VcCascade-TniQ supercomplex
Map dataVcCascade
Sample
  • Complex: protein complex 5
    • Protein or peptide: Cas8
    • Protein or peptide: Cas6
    • Protein or peptide: Cas7
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsChang L / Li Z / Zhang H
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 4, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseJan 29, 2020-
UpdateFeb 19, 2020-
Current statusFeb 19, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0264
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0264
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20910.png

Downloads & links

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Map

FileDownload / File: emd_20910.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVcCascade
Voxel sizeX=Y=Z: 2.1 Å
Density
Contour LevelBy AUTHOR: 0.0264 / Movie #1: 0.0264
Minimum - Maximum-0.02167469 - 0.09408122
Average (Standard dev.)0.0011072487 (±0.00612321)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.12.12.1
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0220.0940.001

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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: Cas8
    • Protein or peptide: Cas6
    • Protein or peptide: Cas7

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Supramolecule #1: protein complex 5

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

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Macromolecule #1: Cas8

MacromoleculeName: Cas8 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MQTLKELIAS NPDDLTTELK RAFRPLTPHI AIDGNELDAL TILVNLTDKT DDQKDLLDRA KCKQKLRDEK WWASCINCVN YRQSHNPKFP DIRSEGVIRT QALGELPSFL LSSSKIPPYH WSYSHDSKYV NKSAFLTNEF CWDGEISCLG ELLKDADHPL WNTLKKLGCS ...String:
MQTLKELIAS NPDDLTTELK RAFRPLTPHI AIDGNELDAL TILVNLTDKT DDQKDLLDRA KCKQKLRDEK WWASCINCVN YRQSHNPKFP DIRSEGVIRT QALGELPSFL LSSSKIPPYH WSYSHDSKYV NKSAFLTNEF CWDGEISCLG ELLKDADHPL WNTLKKLGCS QKTCKAMAKQ LADITLTTIN VTLAPNYLTQ ISLPDSDTSY ISLSPVASLS MQSHFHQRLQ DENRHSAITR FSRTTNMGVT AMTCGGAFRM LKSGAKFSSP PHHRLNSKRS WLTSEHVQSL KQYQRLNKSL IPENSRIALR RKYKIELQNM VRSWFAMQDH TLDSNILIQH LNHDLSYLGA TKRFAYDPAM TKLFTELLKR ELSNSINNGE QHTNGSFLVL PNIRVCGATA LSSPVTVGIP SLTAFFGFVH AFERNINRTT SSFRVESFAI CVHQLHVEKR GLTAEFVEKG DGTISAPATR DDWQCDVVFS LILNTNFAQH IDQDTLVTSL PKRLARGSAK IAIDDFKHIN SFSTLETAIE SLPIEAGRWL SLYAQSNNNL SDLLAAMTED HQLMASCVGY HLLEEPKDKP NSLRGYKHAI AECIIGLINS ITFSSETDPN TIFWSLKNYQ NYLVVQPRSI NDETTDKSSL

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Macromolecule #2: Cas6

MacromoleculeName: Cas6 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: MGSSHHHHHH SQDPNSSMVK WYYKTITFLP ELCNNESLAA KCLRVLHGFN YQYETRNIGV SFPLWCDATV GKKISFVSKN KIELDLLLKQ HYFVQMEQLQ YFHISNTVLV PEDCTYVSFR RCQSIDKLTA AGLARKIRRL EKRALSRGEQ FDPSSFAQKE HTAIAHYHSL ...String:
MGSSHHHHHH SQDPNSSMVK WYYKTITFLP ELCNNESLAA KCLRVLHGFN YQYETRNIGV SFPLWCDATV GKKISFVSKN KIELDLLLKQ HYFVQMEQLQ YFHISNTVLV PEDCTYVSFR RCQSIDKLTA AGLARKIRRL EKRALSRGEQ FDPSSFAQKE HTAIAHYHSL GESSKQTNRN FRLNIRMLSE QPREGNSIFS SYGLSNSENS FQPVPLI

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Macromolecule #3: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString: MADLKLPTNL AYERSIDPSD VCFFVVWPDD RKTPLTYNSR TLLGQMEAAS LAYDVSGQPI KSATAEALAQ GNPHQVDFCH VPYGASHIEC SFSVSFSSEL RQPYKCNSSK VKQTLVQLVE LYETKIGWTE LATRYLMNIC NGKWLWKNTR KAYCWNIVLT PWPWNGEKVG ...String:
MADLKLPTNL AYERSIDPSD VCFFVVWPDD RKTPLTYNSR TLLGQMEAAS LAYDVSGQPI KSATAEALAQ GNPHQVDFCH VPYGASHIEC SFSVSFSSEL RQPYKCNSSK VKQTLVQLVE LYETKIGWTE LATRYLMNIC NGKWLWKNTR KAYCWNIVLT PWPWNGEKVG FEDIRTNYTS RQDFKNNKNW SAIVEMIKTA FSSTDGLAIF EVRATLHLPT NAMVRPSQVF TEKESGSKSK SKTQNSRVFQ STTIDGERSP ILGAFKTGAA IATIDDWYPE ATEPLRVGRF GVHREDVTCY RHPSTGKDFF SILQQAEHYI EVLSANKTPA QETINDMHFL MANLIKGGMF QHKGD

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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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 45000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

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