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- EMDB-22340: Type IV-B CRISPR Complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-22340
TitleType IV-B CRISPR Complex
Map data
Sample
  • Complex: Csf CRISPR Complex
    • Protein or peptide: Csf2 (Cas7)
    • RNA: RNA (31-MER)
    • Protein or peptide: Csf4 (Cas11)
KeywordsCRISPR Complex / IMMUNE SYSTEM-RNA complex
Function / homologyCRISPR type III-associated protein / RAMP superfamily / defense response to virus / RAMP superfamily protein probably involved in DNA repair / Uncharacterized protein
Function and homology information
Biological speciesMycobacterium sp. JS623 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBravo JPK / Taylor DW
Funding support United States, 2 items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160088 United States
CitationJournal: iScience / Year: 2021
Title: Structure of a type IV CRISPR-Cas ribonucleoprotein complex.
Authors: Yi Zhou / Jack P K Bravo / Hannah N Taylor / Jurre A Steens / Ryan N Jackson / Raymond H J Staals / David W Taylor /
Abstract: We reveal the cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein (RNP) complex (Csf) at 3.9-Å resolution. The complex best resembles the type III-A CRISPR Csm effector ...We reveal the cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein (RNP) complex (Csf) at 3.9-Å resolution. The complex best resembles the type III-A CRISPR Csm effector complex, consisting of a Cas7-like (Csf2) filament intertwined with a small subunit (Cas11) filament, but the complex lacks subunits for RNA processing and target DNA cleavage. Surprisingly, instead of assembling around a CRISPR-derived RNA (crRNA), the complex assembles upon heterogeneous RNA of a regular length arranged in a pseudo-A-form configuration. These findings provide a high-resolution glimpse into the assembly and function of enigmatic type IV CRISPR systems, expanding our understanding of class I CRISPR-Cas system architecture, and suggesting a function for type IV-B RNPs that may be distinct from other class 1 CRISPR-associated systems.
History
DepositionJul 21, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jhy
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22340.png

Downloads & links

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Map

FileDownload / File: emd_22340.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 288 pix.
= 316.8 Å		1.1 Å/pix.
x 288 pix.
= 316.8 Å		1.1 Å/pix.
x 288 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-2.1174994 - 3.2306864
Average (Standard dev.)0.00030804813 (±0.0347061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-2.1173.2310.000

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Supplemental data

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Sample components

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Entire : Csf CRISPR Complex

EntireName: Csf CRISPR Complex
Components
  • Complex: Csf CRISPR Complex
    • Protein or peptide: Csf2 (Cas7)
    • RNA: RNA (31-MER)
    • Protein or peptide: Csf4 (Cas11)

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Supramolecule #1: Csf CRISPR Complex

SupramoleculeName: Csf CRISPR Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mycobacterium sp. JS623 (bacteria)

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Macromolecule #1: Csf2 (Cas7)

MacromoleculeName: Csf2 (Cas7) / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium sp. JS623 (bacteria)
Molecular weightTheoretical: 32.085174 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSWSHPQFEK GAMTLSTIRW DVDIIAQSSI VHRDDYTSVG SDTFTLFRRE KIIGPDGQIL QIPLISGSSF RGVLRRVGEA LTAEVLGYE DVALPVPAAH LLTNGGRLAK SAHPLTDEEE RNLKELLPQI AVFGGAASGR VMSGLLSVSK VLPEIAELAH L LPRPPHST ...String:
MSWSHPQFEK GAMTLSTIRW DVDIIAQSSI VHRDDYTSVG SDTFTLFRRE KIIGPDGQIL QIPLISGSSF RGVLRRVGEA LTAEVLGYE DVALPVPAAH LLTNGGRLAK SAHPLTDEEE RNLKELLPQI AVFGGAASGR VMSGLLSVSK VLPEIAELAH L LPRPPHST PLLPAVLSVA DESFTHLPDH RPSTGGAPRT DHADGSPLGR FAIETLPAGT RLQTWARLDN ATEHQAAFFD NV LSTFAAH GHLGGRSAAG HGQVTATVTA TALRGSLPRP TVDWVNQLAD DRDAAIAALT RLT

UniProtKB: RAMP superfamily protein probably involved in DNA repair

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Macromolecule #3: Csf4 (Cas11)

MacromoleculeName: Csf4 (Cas11) / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium sp. JS623 (bacteria)
Molecular weightTheoretical: 17.939254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTPTPTQVW RATVPELPPL VDEAGDTGSA TARAADTAER LLLLLHYSID WESSWVADPK HRKTYWDELL PGRVRRAAYR ADTLDRWWS EVAGQLGAPA PRHRDRRLEL ATLLREPALP VITVLRDSLP ALLLRVRIIA EAVAAQRGNN SAATSSADPN E PA

UniProtKB: Uncharacterized protein

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Macromolecule #2: RNA (31-MER)

MacromoleculeName: RNA (31-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Mycobacterium sp. JS623 (bacteria)
Molecular weightTheoretical: 9.561382 KDa
SequenceString:
AUUUUUUUUU AUUAUUUUUA UUUUUUAUUU U

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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

Concentration0.3 mg/mL
BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 296319
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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