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- EMDB-26084: Cascade complex from type I-A CRISPR-Cas system -

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Basic information

Entry
Database: EMDB / ID: EMD-26084
TitleCascade complex from type I-A CRISPR-Cas system
Map data
Sample
  • Complex: full R-loop state of Cas3-Cascade complex from Pyrococcus furiosus type I-A CRISPR/Cas system
    • Protein or peptide: CRISPR-associated helicase Cas3
    • Protein or peptide: Cas8a
    • Protein or peptide: Cas11a
    • Protein or peptide: Cas7a
    • Protein or peptide: Cas5a
    • Protein or peptide: CRISPR-associated endonuclease Cas3-HD
    • RNA: crRNA (44-MER)
    • DNA: Target strand DNA (44-MER)
    • DNA: Non-Target strand DNA (25-MER)
  • Ligand: NICKEL (II) ION
KeywordsCRISPR / cascade / Cas3 / type I-A / genome editing / DNA targeting / RNA BINDING PROTEIN
Function / homology
Function and homology information


catalytic activity, acting on DNA / DNA conformation change / exonuclease activity / defense response to virus / endonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds / ATP binding / metal ion binding
Similarity search - Function
CRISPR-associated protein, MJ0385 / CRISPR-associated protein (Cas_Csa4) / CRISPR-associated protein, Cas5a type / : / CRISPR-associated protein Cas7/Cst2/DevR, subtype I-a/Apern / CRISPR-associated protein Cas7/Cst2/DevR / : / CRISPR-associated negative auto-regulator DevR/Csa2 / Helicase Cas3, CRISPR-associated, core / Cas3, HD domain ...CRISPR-associated protein, MJ0385 / CRISPR-associated protein (Cas_Csa4) / CRISPR-associated protein, Cas5a type / : / CRISPR-associated protein Cas7/Cst2/DevR, subtype I-a/Apern / CRISPR-associated protein Cas7/Cst2/DevR / : / CRISPR-associated negative auto-regulator DevR/Csa2 / Helicase Cas3, CRISPR-associated, core / Cas3, HD domain / CRISPR-associated nuclease/helicase Cas3, C-terminal / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / HD Cas3-type domain profile. / CRISPR-associated protein Cas5, N-terminal / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CRISPR-associated helicase Cas3 / Type I-A CRISPR-associated protein Cas5 / Uncharacterized protein / Type I-A CRISPR-associated protein Cas7/Csa2 / CRISPR-associated endonuclease Cas3-HD / Type I-A CRISPR-associated protein Cas8a2/Csa4
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria) / Pyrococcus furiosus DSM 3638 (archaea) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHu C / Ni D
Funding support United States, Switzerland, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118117 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118160 United States
Swiss National Science FoundationNCCR Switzerland
CitationJournal: Mol Cell / Year: 2022
Title: Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools.
Authors: Chunyi Hu / Dongchun Ni / Ki Hyun Nam / Sonali Majumdar / Justin McLean / Henning Stahlberg / Michael P Terns / Ailong Ke /
Abstract: Type I CRISPR-Cas systems typically rely on a two-step process to degrade DNA. First, an RNA-guided complex named Cascade identifies the complementary DNA target. The helicase-nuclease fusion enzyme ...Type I CRISPR-Cas systems typically rely on a two-step process to degrade DNA. First, an RNA-guided complex named Cascade identifies the complementary DNA target. The helicase-nuclease fusion enzyme Cas3 is then recruited in trans for processive DNA degradation. Contrary to this model, here, we show that type I-A Cascade and Cas3 function as an integral effector complex. We provide four cryoelectron microscopy (cryo-EM) snapshots of the Pyrococcus furiosus (Pfu) type I-A effector complex in different stages of DNA recognition and degradation. The HD nuclease of Cas3 is autoinhibited inside the effector complex. It is only allosterically activated upon full R-loop formation, when the entire targeted region has been validated by the RNA guide. The mechanistic insights inspired us to convert Pfu Cascade-Cas3 into a high-sensitivity, low-background, and temperature-activated nucleic acid detection tool. Moreover, Pfu CRISPR-Cas3 shows robust bi-directional deletion-editing activity in human cells, which could find usage in allele-specific inactivation of disease-causing mutations.
History
DepositionJan 28, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26084.png

Downloads & links

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Map

FileDownload / File: emd_26084.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 300 pix.
= 372. Å		1.24 Å/pix.
x 300 pix.
= 372. Å		1.24 Å/pix.
x 300 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.145
Minimum - Maximum-0.42493927 - 1.0326657
Average (Standard dev.)-0.0015686031 (±0.038146064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cas3 part local refinement

Fileemd_26084_additional_1.map
AnnotationCas3 part local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_26084_additional_2.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : full R-loop state of Cas3-Cascade complex from Pyrococcus furiosu...

EntireName: full R-loop state of Cas3-Cascade complex from Pyrococcus furiosus type I-A CRISPR/Cas system
Components
  • Complex: full R-loop state of Cas3-Cascade complex from Pyrococcus furiosus type I-A CRISPR/Cas system
    • Protein or peptide: CRISPR-associated helicase Cas3
    • Protein or peptide: Cas8a
    • Protein or peptide: Cas11a
    • Protein or peptide: Cas7a
    • Protein or peptide: Cas5a
    • Protein or peptide: CRISPR-associated endonuclease Cas3-HD
    • RNA: crRNA (44-MER)
    • DNA: Target strand DNA (44-MER)
    • DNA: Non-Target strand DNA (25-MER)
  • Ligand: NICKEL (II) ION

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Supramolecule #1: full R-loop state of Cas3-Cascade complex from Pyrococcus furiosu...

SupramoleculeName: full R-loop state of Cas3-Cascade complex from Pyrococcus furiosus type I-A CRISPR/Cas system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9 / Details: full R-loop state
Source (natural)Organism: Geobacter sulfurreducens (bacteria)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: CRISPR-associated helicase Cas3

MacromoleculeName: CRISPR-associated helicase Cas3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 61.412555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ELTGFEPYDY QLRAWEKIRE IMNNGGKVII EVPTAGGKTE TAVMPFFAGI YNNNWPVARL VYVLPTRSLV EKQAERLRNL VYKLLQLKG KSKEEAEKLA RELVVVEYGL EKTHAFLGWV VVTTWDAFLY GLAAHRTVGN RFTFPAGAIA QSLVIFDEVQ M YQDESMYM ...String:
ELTGFEPYDY QLRAWEKIRE IMNNGGKVII EVPTAGGKTE TAVMPFFAGI YNNNWPVARL VYVLPTRSLV EKQAERLRNL VYKLLQLKG KSKEEAEKLA RELVVVEYGL EKTHAFLGWV VVTTWDAFLY GLAAHRTVGN RFTFPAGAIA QSLVIFDEVQ M YQDESMYM PRLLSLVVGI LEEANVPLVI MSATIPSKLR EMIAGDTEVI TVDKNDKNKP SKGNVKVRLV EGDITDVLND IK KILKNGK KVLVVRNTVR KAVETYQVLK KKLNDTLANP SDALLIHSRF TIGDRREKER ALDSARLIVA TQVVEAGLDL PNV GLVVTD IAPLDALIQR IGRCARRPGE EGEGIILIPA AAAAAAAAAA AAAAAAAAAA AAAAAAAVVT STNEYDRVVE IHYG EGKKN FVYVGDIDTA RRVLEKKRSK KLPKDLYIIP YSVSPYPDPL VLLTTYDELS KIGEYLADTT KARKALDRVY KFHYE NNIV PKEFASYIYF KELKLFSAPP EYEKAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAI DAKYYNSELA AAAAAA AAA AAAAAAAAA

UniProtKB: CRISPR-associated helicase Cas3

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Macromolecule #2: Cas8a

MacromoleculeName: Cas8a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 38.800719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FNEFKTPQID PIFDLYVAYG YVVSLIRGGA KEATLIPHGA SYLIQTDVSN EEFRHGLVDA LSSMLSLHIA LARHSPREGG KLVSDADFS AGANINNVYW DSVPRNLEKL MKDLEKKRSV KGTATIPITL MPSAGKYMLK HFGVQGGNPI KVDLLNYALA W VGFHYYTP ...String:
FNEFKTPQID PIFDLYVAYG YVVSLIRGGA KEATLIPHGA SYLIQTDVSN EEFRHGLVDA LSSMLSLHIA LARHSPREGG KLVSDADFS AGANINNVYW DSVPRNLEKL MKDLEKKRSV KGTATIPITL MPSAGKYMLK HFGVQGGNPI KVDLLNYALA W VGFHYYTP YIKYAKGDTT WIHIYQIAPV EEVDMISILS LKDLKMHLPH YYESNLDFLI NRRLALLYHL LHSEALELFT EK EFVIHSY TLERSGNNQA IRSFEEEEIG KLMDFLWKLK RRDFYHAIKF IDDLLKKATE GALALIDAIM NERLEGFYTA LKL GKKAGV VSSREIVAAL EDIIC

UniProtKB: Type I-A CRISPR-associated protein Cas8a2/Csa4

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Macromolecule #3: Cas11a

MacromoleculeName: Cas11a / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 12.208933 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GGWIRNIGRY LSYLVDDTFE EYAYDVVDGI AKARTQEELL EGVYKALRLA PKLKKKAESK GCPPPRIPSP EDIEALEEKV EQLSNPKDL RKLAVSLALW AFASWNNCP

UniProtKB: Uncharacterized protein

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Macromolecule #4: Cas7a

MacromoleculeName: Cas7a / type: protein_or_peptide / ID: 4 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 36.989148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYVRISGRIR LNAHSLNAQG GGGTNYIEIT KTKVTVRTEN GWTVVEVPAI TGNMLKHWHF VGFVDYFKTT PYGVNLTERA LRYNGTRFG QGETTATKAN GATVQLNDEA TIIKELADAD VHGFLAPKTG RRRVSLVKAS FILPTEDFIK EVEGERLITA I KHNRVDVD ...String:
MYVRISGRIR LNAHSLNAQG GGGTNYIEIT KTKVTVRTEN GWTVVEVPAI TGNMLKHWHF VGFVDYFKTT PYGVNLTERA LRYNGTRFG QGETTATKAN GATVQLNDEA TIIKELADAD VHGFLAPKTG RRRVSLVKAS FILPTEDFIK EVEGERLITA I KHNRVDVD EKGAIGSSKE GTAQMLFSRE YATGLYGFSI VLDLGLVGIP QGLPVKFEEN QPRPNIVIDP NERKARIESA LK ALIPMLS GYIGANLARS FPVFKVEELV AIASEGPIPA LVHGFYEDYI EANRSIIKNA RALGFNIEVF TYNVDLGEDI EAT KVSSVE ELVANLVKMV

UniProtKB: Type I-A CRISPR-associated protein Cas7/Csa2

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Macromolecule #5: Cas5a

MacromoleculeName: Cas5a / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 29.147219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDILLVCLRF PFFSVAKRSY QVRTSFLLPP PSALKGALAK GLILLKPEKY ASSSLDEAAL KAIKEIESKL VDIKAVSVAP LSPLIRNAF LLKRLRNLES GSNAEKSDAM RREYTFTREL LVAYIFKNLT QEEKNLYLKA AMLIDVIGDT ESLATPVWAS F VKPEDKKA ...String:
MDILLVCLRF PFFSVAKRSY QVRTSFLLPP PSALKGALAK GLILLKPEKY ASSSLDEAAL KAIKEIESKL VDIKAVSVAP LSPLIRNAF LLKRLRNLES GSNAEKSDAM RREYTFTREL LVAYIFKNLT QEEKNLYLKA AMLIDVIGDT ESLATPVWAS F VKPEDKKA PLAFSAPYTE IYSLLSSKIQ AKGKIRMYIE KMRVSPEYSK TKGPQEEIFY LPIEERRYKR IVYYARIYPP EV EKALTVD GEVLGIWIP

UniProtKB: Type I-A CRISPR-associated protein Cas5

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Macromolecule #6: CRISPR-associated endonuclease Cas3-HD

MacromoleculeName: CRISPR-associated endonuclease Cas3-HD / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 24.778203 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SCKAFQGQTL REHIEAMLAA WEIVKNKYIP SIIRVMKTVG VKFTEEDADK FMKTLIILHD VGKCSEVYQK HLSNNEPLRG FRHELVSAY YAYNILKDMF KDETIAFIGA LVVMMHHEPI LMGQIRSLDK EELTPEVVLD KLRTFNGVME GTESFIKSMI K EKLGVIPK ...String:
SCKAFQGQTL REHIEAMLAA WEIVKNKYIP SIIRVMKTVG VKFTEEDADK FMKTLIILHD VGKCSEVYQK HLSNNEPLRG FRHELVSAY YAYNILKDMF KDETIAFIGA LVVMMHHEPI LMGQIRSLDK EELTPEVVLD KLRTFNGVME GTESFIKSMI K EKLGVIPK VPSPTQEDVL REVIRLSVLA RHRPDSGKLR MVVGALLIPL VCDYKGAAAA A

UniProtKB: CRISPR-associated endonuclease Cas3-HD

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Macromolecule #7: crRNA (44-MER)

MacromoleculeName: crRNA (44-MER) / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli) / Strain: DE3
Molecular weightTheoretical: 14.028332 KDa
SequenceString:
AUUGAAAGAG UGCUUCCCCA AACCCUUAAC UGGUUGUAAC AGUU

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Macromolecule #8: Target strand DNA (44-MER)

MacromoleculeName: Target strand DNA (44-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.692797 KDa
SequenceString:
(DT)(DA)(DA)(DA)(DC)(DT)(DG)(DT)(DT)(DA) (DC)(DA)(DA)(DC)(DC)(DA)(DG)(DT)(DT)(DA) (DA)(DG)(DG)(DG)(DT)(DT)(DG)(DG)(DG) (DG)(DG)(DA)(DA)(DG)(DC)(DA)(DC)(DT)(DG) (DG) (DG)(DT)(DC)(DT)

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Macromolecule #9: Non-Target strand DNA (25-MER)

MacromoleculeName: Non-Target strand DNA (25-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.727109 KDa
SequenceString:
(DA)(DG)(DA)(DC)(DC)(DC)(DA)(DG)(DT)(DT) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)

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Macromolecule #10: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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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 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 6 seconds.

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Electron microscopy

MicroscopeTFS TALOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 1209 / Average exposure time: 2.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

Detailsfull R-loop state of type I-A CRISPR/cas complex
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 44773
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-7tra:
Cascade complex from type I-A CRISPR-Cas system

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