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- EMDB-7347: CRISPR RNA-guided surveillance complex, pre-nicking -

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Basic information

Entry
Database: EMDB / ID: EMD-7347
TitleCRISPR RNA-guided surveillance complex, pre-nicking
Map dataCRISPR RNA-guided surveillance complex with Cas3 bound in its pre-nicking state
Sample
  • Complex: CRISPR RNA-guided surveillance complex with Cas3 bound in its pre-nicking state
    • Protein or peptide: CRISPR-associated helicase, Cas3 family
    • Protein or peptide: CRISPR-associated protein, Cse1 family
    • Protein or peptide: CRISPR-associated protein, Cse4 family
    • Protein or peptide: Uncharacterized protein
    • RNA: crRNA
    • DNA: Target strand
    • Protein or peptide: CRISPR-associated protein, Cas5e family
    • DNA: Nontarget strand
    • Protein or peptide: CRISPR-associated protein, Cse3 family
  • Ligand: FE (III) ION
KeywordsCRISPR-Cas / Cascade / Cas3 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / helicase activity / defense response to virus / hydrolase activity / RNA binding / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Cas3, C-terminal / Cas3 C-terminal domain / CRISPR-associated protein, CT1975 / CT1975-like protein / CRISPR-associated protein, CasD / Helicase Cas3, CRISPR-associated, core / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein Cse1 ...Cas3, C-terminal / Cas3 C-terminal domain / CRISPR-associated protein, CT1975 / CT1975-like protein / CRISPR-associated protein, CasD / Helicase Cas3, CRISPR-associated, core / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / Cas3, HD domain / HD Cas3-type domain profile. / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / CRISPR-associated protein Cas5, N-terminal / helicase superfamily c-terminal domain / Helicase, C-terminal / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CRISPR-associated helicase, Cas3 family / CRISPR-associated protein, Cse1 family / CRISPR-associated protein, Cse2 family / CRISPR-associated protein, Cse4 family / CRISPR-associated protein, Cas5e family / CRISPR-associated protein, Cse3 family
Similarity search - Component
Biological speciesThermobifida fusca (strain YX) (bacteria) / Thermobifida fusca (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsXiao Y / Luo M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118174 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102543 United States
CitationJournal: Science / Year: 2018
Title: Structure basis for RNA-guided DNA degradation by Cascade and Cas3.
Authors: Yibei Xiao / Min Luo / Adam E Dolan / Maofu Liao / Ailong Ke /
Abstract: Type I CRISPR-Cas system features a sequential target-searching and degradation process on double-stranded DNA by the RNA-guided Cascade (CRISPR associated complex for antiviral defense) complex and ...Type I CRISPR-Cas system features a sequential target-searching and degradation process on double-stranded DNA by the RNA-guided Cascade (CRISPR associated complex for antiviral defense) complex and the nuclease-helicase fusion enzyme Cas3, respectively. Here, we present a 3.7-angstrom-resolution cryo-electron microscopy (cryo-EM) structure of the Type I-E Cascade/R-loop/Cas3 complex, poised to initiate DNA degradation. Cas3 distinguishes Cascade conformations and only captures the R-loop-forming Cascade, to avoid cleaving partially complementary targets. Its nuclease domain recruits the nontarget strand (NTS) DNA at a bulged region for the nicking of single-stranded DNA. An additional 4.7-angstrom-resolution cryo-EM structure captures the postnicking state, in which the severed NTS retracts to the helicase entrance, to be threaded for adenosine 5'-triphosphate-dependent processive degradation. These snapshots form the basis for understanding RNA-guided DNA degradation in Type I-E CRISPR-Cas systems.
History
DepositionJan 17, 2018-
Header (metadata) releaseFeb 7, 2018-
Map releaseJun 27, 2018-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6c66
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7347.png

Downloads & links

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Map

FileDownload / File: emd_7347.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCRISPR RNA-guided surveillance complex with Cas3 bound in its pre-nicking state
Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.04
Minimum - Maximum-0.10162261 - 0.21208328
Average (Standard dev.)-0.00003452048 (±0.009961365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 317.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z317.440317.440317.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1020.212-0.000

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Supplemental data

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Sample components

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Entire : CRISPR RNA-guided surveillance complex with Cas3 bound in its pre...

EntireName: CRISPR RNA-guided surveillance complex with Cas3 bound in its pre-nicking state
Components
  • Complex: CRISPR RNA-guided surveillance complex with Cas3 bound in its pre-nicking state
    • Protein or peptide: CRISPR-associated helicase, Cas3 family
    • Protein or peptide: CRISPR-associated protein, Cse1 family
    • Protein or peptide: CRISPR-associated protein, Cse4 family
    • Protein or peptide: Uncharacterized protein
    • RNA: crRNA
    • DNA: Target strand
    • Protein or peptide: CRISPR-associated protein, Cas5e family
    • DNA: Nontarget strand
    • Protein or peptide: CRISPR-associated protein, Cse3 family
  • Ligand: FE (III) ION

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Supramolecule #1: CRISPR RNA-guided surveillance complex with Cas3 bound in its pre...

SupramoleculeName: CRISPR RNA-guided surveillance complex with Cas3 bound in its pre-nicking state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Thermobifida fusca (strain YX) (bacteria)

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Macromolecule #1: CRISPR-associated helicase, Cas3 family

MacromoleculeName: CRISPR-associated helicase, Cas3 family / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermobifida fusca (strain YX) (bacteria) / Strain: YX
Molecular weightTheoretical: 104.039219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPEHDSTDDK HGIPPLDLRF WAKERGLRGK TYPLVCHSLD AAAAALVLWN EYLSPGLRDT IASSMETDEE HAGHCIAFWA GLHDIGKLT REFQQQIAID LSAYPGEELS GEQRSHAAAT GKWLPFALPS LGYPNGGLVT GLVAQMLGGH HGTFHPHPSF Q SRNPLAEF ...String:
MPEHDSTDDK HGIPPLDLRF WAKERGLRGK TYPLVCHSLD AAAAALVLWN EYLSPGLRDT IASSMETDEE HAGHCIAFWA GLHDIGKLT REFQQQIAID LSAYPGEELS GEQRSHAAAT GKWLPFALPS LGYPNGGLVT GLVAQMLGGH HGTFHPHPSF Q SRNPLAEF GFSSPHWEKQ RHALLHAVFD ATGRPTPPDM LDGPTASVVC GLVILADWLV SQEDFLLERL TSLPADGSAS AL RAHFETS LRRIPSLLDA AGLRPITVPP ATFTESFPHL SKPNGLQASL AKHLPCLCTG PGLVLITAPM GEGKTEAAYH VAD LLGKAT GRPGRFLALP TMATADQMHT RLKEYARYRV ENTDLPRSST LALLHSMAWL NPDYAPADLP GVSKVLSNLG HRDP FAATD WLMGRKRGLL APWAVGTIDQ ALMAVLRAKH NALRLFGLAG KVVVVDEAHA VDPYMQVLLE QLLRWLGTLD VPVVL LSAT LHHSIANSLV KAYLEGARGR RWNRSEPQPV SEVSYPGWLH VDARIGKVTR SSDVDPLPIA TTPRKPLEVR LVDVPV KEG ALNRSTVLAK ELTPLVKQGG CAAIICTTVA EAQGVYDLLS QWFATLGEDA PDLYLLHSRF PNRQRTEITA TIVDLFG KE GAQSGRRPTR GAVLVATQVV EQSLDLDVDL MISDLAPVSL LLQRAGRCWR HEHLGIINRP QWAKQPELVV LTPEQNGD A DRAPWFPRSW TSVYPLALLQ RTYTLLRRRN GAPVQIPEDV QQLVDDVYDD DSLAEDLEAD MERMGEELAQ RGLARNAVI PDPDDAEDNL NGLTEFSFDV DEHVLATRFG AGSVRVLCYY VDTAGNRWLD PECTVEFPEQ GTGREGRFTM ADCRDLVART IPVRMGPWA SQLTEDNHPP EAWRESFYLR DLVLIPQRVT DEGAVLPTET GGREWLLDPC KGLIF

UniProtKB: CRISPR-associated helicase, Cas3 family

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Macromolecule #2: CRISPR-associated protein, Cse1 family

MacromoleculeName: CRISPR-associated protein, Cse1 family / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermobifida fusca (strain YX) (bacteria) / Strain: YX
Molecular weightTheoretical: 61.433297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLSVALCFLV GGAIPSPPSF DVTIAPWLIA RSRDVLAAPE MLGLRDVLIR SHELSDVEIP LPPGAAVLWR ILALITARIT GLDQPPNKN PKRKWQARRS QILSKGRLDP EAVDAYFADY SERFDLFHPE RPWLQDPRLR EECPKTSGVN KLAWGRTAGE N QVWLGGHH ...String:
MLSVALCFLV GGAIPSPPSF DVTIAPWLIA RSRDVLAAPE MLGLRDVLIR SHELSDVEIP LPPGAAVLWR ILALITARIT GLDQPPNKN PKRKWQARRS QILSKGRLDP EAVDAYFADY SERFDLFHPE RPWLQDPRLR EECPKTSGVN KLAWGRTAGE N QVWLGGHH HDLDPHPLDS AEAVWHLLAT LGYGPSGMCT ARVVRGRSER NVTAGPLRGT VSYHPLGRTL FESLILNIPY PG TGAADLA FWEQPELNDP LGLPEESAGL AGILRLDHFR HAVLLHPSPD GSHVVDAWVT WAWRERNISP ELDPYLIYQT SKE GRVYPR PAEAERAIWR DLDALLHYGE DGNYRPTILD NCTPLAQVPQ EVLDSLRLRA FGFDQDGQAR DKQWFTATTP AVLR WLADR ETDDNENARI VRRITLARKA AEALGRRLEK ACKEAWKESN SPSSTSSGTN AKTETGVGPW VQHGMSRYWA KAEPV FWNI VYDRPAQGYT PGMAGPGNAF NLVALAAYDE VTGPYCERPR VAKVVERHRS TLFSNWTPKQ DKEAA

UniProtKB: CRISPR-associated protein, Cse1 family

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Macromolecule #3: CRISPR-associated protein, Cse4 family

MacromoleculeName: CRISPR-associated protein, Cse4 family / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermobifida fusca (strain YX) (bacteria) / Strain: YX
Molecular weightTheoretical: 41.043043 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTFVDIHAIQ TLPYSNINRD DLGSPKTVVY GGKERTRVSS QSWKRAVRHE VEARLGDKAV RTRRIISEIA KRLRERGWDA DLADAGARQ VVLSVGKKSG IKLEKEKDSE APATSVLFYL PVPAIDELAA IADEHRDAVA KEAAKKTPKG ILPADRITEV L KSRNVSVN ...String:
MTFVDIHAIQ TLPYSNINRD DLGSPKTVVY GGKERTRVSS QSWKRAVRHE VEARLGDKAV RTRRIISEIA KRLRERGWDA DLADAGARQ VVLSVGKKSG IKLEKEKDSE APATSVLFYL PVPAIDELAA IADEHRDAVA KEAAKKTPKG ILPADRITEV L KSRNVSVN LFGRMLAELP STEVDGAVQF AHAFTVHGTT VEVDFFTAVD DIPKENDHGS GHMNAGQFSA GTFYRYANVN LD RLVENTG DAQTARTAVA EFLRAFLSTV PSGKQNATAA MTLPDLVHIA VRFDRPISFA PAFETALYGS DGYTLRACQE LNN YAERLR EVWPDDAIRG YATVENKTDL AALGERYDSY PALIDAMVAA AFEGERE

UniProtKB: CRISPR-associated protein, Cse4 family

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Macromolecule #4: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermobifida fusca (strain YX) (bacteria) / Strain: YX
Molecular weightTheoretical: 27.446613 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSDYILQHA DALVKRVSKL IVNEPAARAA LRRGVGLAPE DPRMLAAHRV VAPYVPVPTD YDVDRRRAAS LWDVHAVERA FYAVAAIMA AQPRSARDQE AEATEEQTGE PQDSEALTEP TPAEESSATK DGKPDRRPNL GVSLAQAVFD KGLNADSTEQ R LHLIARQN ...String:
MNSDYILQHA DALVKRVSKL IVNEPAARAA LRRGVGLAPE DPRMLAAHRV VAPYVPVPTD YDVDRRRAAS LWDVHAVERA FYAVAAIMA AQPRSARDQE AEATEEQTGE PQDSEALTEP TPAEESSATK DGKPDRRPNL GVSLAQAVFD KGLNADSTEQ R LHLIARQN LDGVHRHLPR LVLYLRSDQV HIDWGILIRD LARWGHTPRH VAREWVQDYH RTLETLTRQA EQKNKNNTTD EE AEAA

UniProtKB: CRISPR-associated protein, Cse2 family

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Macromolecule #7: CRISPR-associated protein, Cas5e family

MacromoleculeName: CRISPR-associated protein, Cas5e family / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermobifida fusca (strain YX) (bacteria) / Strain: YX
Molecular weightTheoretical: 28.27926 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGFLLRLAG PMQSWGEHSM FGERDTLPYP SRSGLIGMFA AAQGVRRGDP LDRYKELKFT VRVDRPGVRL VDFHTIGGGL PKERTVPTA AGERRDPKKA TIVTSRSYLA DAVFTVAVTG PEADTIADAL AAPYWQPYLG RRAFVPDPLL VLRRRVADPV R ELVEAVPL ...String:
MSGFLLRLAG PMQSWGEHSM FGERDTLPYP SRSGLIGMFA AAQGVRRGDP LDRYKELKFT VRVDRPGVRL VDFHTIGGGL PKERTVPTA AGERRDPKKA TIVTSRSYLA DAVFTVAVTG PEADTIADAL AAPYWQPYLG RRAFVPDPLL VLRRRVADPV R ELVEAVPL PHRRVEEDAA TVLVDLIYEE GEYPDTRTLT VLNDVPLSFD SKSRRYSTRQ IRVVPTEVPA TLVAGPGRDY QN KLFTYVK QCAEEAA

UniProtKB: CRISPR-associated protein, Cas5e family

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Macromolecule #9: CRISPR-associated protein, Cse3 family

MacromoleculeName: CRISPR-associated protein, Cse3 family / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermobifida fusca (strain YX) (bacteria) / Strain: YX
Molecular weightTheoretical: 26.327938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTWLTKIVPD LRYRQTRADF RTAGNLHRKL IRLSSDLGEE RIANPRQQSG LLFRIEETRN ELYLLVQSHS PLRVDRLGPG YHGVQMRNL DPFLARLDKG SRVRYRIVAS PTKRLGRSEN NTQRLGLKEP PKKPREYTWA LRGAAAEEWW HSRAAANGLE L LSTYAQTL ...String:
MTWLTKIVPD LRYRQTRADF RTAGNLHRKL IRLSSDLGEE RIANPRQQSG LLFRIEETRN ELYLLVQSHS PLRVDRLGPG YHGVQMRNL DPFLARLDKG SRVRYRIVAS PTKRLGRSEN NTQRLGLKEP PKKPREYTWA LRGAAAEEWW HSRAAANGLE L LSTYAQTL DDVRDPGTAD RSRKIRHPAV RFDGEAVISD VDAVRHAVLN GIGRGKSYGC GLLSLALIEE GEHG

UniProtKB: CRISPR-associated protein, Cse3 family

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Macromolecule #5: crRNA

MacromoleculeName: crRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Thermobifida fusca (bacteria)
Molecular weightTheoretical: 19.790793 KDa
SequenceString:
AUGGACCGCC AGUGAUAAGU GGAAUGCCAU GUGGGCUGUC GUGAGCCCCA CGCACGUGGG G

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Macromolecule #6: Target strand

MacromoleculeName: Target strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Thermobifida fusca (bacteria)
Molecular weightTheoretical: 16.801725 KDa
SequenceString: (DG)(DC)(DG)(DT)(DC)(DC)(DA)(DG)(DG)(DC) (DG)(DA)(DC)(DA)(DG)(DC)(DC)(DC)(DA)(DC) (DA)(DT)(DG)(DG)(DC)(DA)(DT)(DT)(DC) (DC)(DA)(DC)(DT)(DT)(DA)(DT)(DC)(DA)(DC) (DT) (DG)(DG)(DC)(DT)(DT)(DC) ...String:
(DG)(DC)(DG)(DT)(DC)(DC)(DA)(DG)(DG)(DC) (DG)(DA)(DC)(DA)(DG)(DC)(DC)(DC)(DA)(DC) (DA)(DT)(DG)(DG)(DC)(DA)(DT)(DT)(DC) (DC)(DA)(DC)(DT)(DT)(DA)(DT)(DC)(DA)(DC) (DT) (DG)(DG)(DC)(DT)(DT)(DC)(DG)(DT) (DC)(DC)(DG)(DC)(DG)(DC)(DG)

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Macromolecule #8: Nontarget strand

MacromoleculeName: Nontarget strand / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Thermobifida fusca (bacteria)
Molecular weightTheoretical: 17.09992 KDa
SequenceString: (DC)(DG)(DC)(DG)(DC)(DG)(DG)(DA)(DC)(DG) (DA)(DA)(DG)(DC)(DC)(DA)(DG)(DT)(DG)(DA) (DT)(DA)(DA)(DG)(DT)(DG)(DG)(DA)(DA) (DT)(DG)(DC)(DC)(DA)(DT)(DG)(DT)(DG)(DG) (DG) (DC)(DT)(DG)(DT)(DC)(DG) ...String:
(DC)(DG)(DC)(DG)(DC)(DG)(DG)(DA)(DC)(DG) (DA)(DA)(DG)(DC)(DC)(DA)(DG)(DT)(DG)(DA) (DT)(DA)(DA)(DG)(DT)(DG)(DG)(DA)(DA) (DT)(DG)(DC)(DC)(DA)(DT)(DG)(DT)(DG)(DG) (DG) (DC)(DT)(DG)(DT)(DC)(DG)(DC)(DC) (DT)(DG)(DG)(DA)(DC)(DG)(DC)

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Macromolecule #10: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 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 / Details: 10 mM HEPES pH 7.5, 150 mM NaCl, 5 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.7 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 105.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1428 / Average electron dose: 8.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 322268
Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 51889

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-6c66:
CRISPR RNA-guided surveillance complex, pre-nicking

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