+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9535 | |||||||||
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Title | Cryo-EM Structure of the PaeCas3-AcrF3 complex | |||||||||
Map data | Cryo-EM structure of PaeCas3-AcrF3 complex | |||||||||
Sample |
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Function / homology | Function and homology information helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) / Pseudomonas phage JBD5 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Zhang X / Ma J / Wang Y / Wang J | |||||||||
Citation | Journal: Cell Res / Year: 2016 Title: A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR/Cas responses. Authors: Jiuyu Wang / Jun Ma / Zhi Cheng / Xu Meng / Lilan You / Min Wang / Xinzheng Zhang / Yanli Wang / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9535.map.gz | 9.7 MB | EMDB map data format | |
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Header (meta data) | emd-9535-v30.xml emd-9535.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_9535.png | 56.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9535 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9535 | HTTPS FTP |
-Related structure data
Related structure data | 5gqhMC 5gnfC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9535.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of PaeCas3-AcrF3 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PaeCas3-AcrF3 complex
Entire | Name: PaeCas3-AcrF3 complex |
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Components |
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-Supramolecule #1: PaeCas3-AcrF3 complex
Supramolecule | Name: PaeCas3-AcrF3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 158 kDa/nm |
-Supramolecule #2: type I-F CRISPR-associated nuclease/helicase Cas3
Supramolecule | Name: type I-F CRISPR-associated nuclease/helicase Cas3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Recombinant expression | Organism: Escherichia Coli BL21(DE3) (bacteria) / Recombinant plasmid: pET |
-Supramolecule #3: anti-CRISPR protein 3 (AcrF3)
Supramolecule | Name: anti-CRISPR protein 3 (AcrF3) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Pseudomonas phage JBD5 (virus) |
Recombinant expression | Organism: Escherichia Coli BL21(DE3) (bacteria) / Recombinant plasmid: pET |
-Macromolecule #1: type I-F CRISPR-associated nuclease/helicase Cas3
Macromolecule | Name: type I-F CRISPR-associated nuclease/helicase Cas3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Recombinant expression | Organism: Escherichia Coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SQDPMNILLV SQCEKRALSE TRRILDQFAE RRGERTWQTP ITQAGLDTLR RLLKKSARRN TAVACHWIRG RDHSELLWIV GDASRFNAQG AVPTNRTCRD ILRKEDENDW HSAEDIRLLT VMAALFHDIG KASQAFQAKL RNRGKPMADA YRHEWVSLRL ...String: MGSSHHHHHH SQDPMNILLV SQCEKRALSE TRRILDQFAE RRGERTWQTP ITQAGLDTLR RLLKKSARRN TAVACHWIRG RDHSELLWIV GDASRFNAQG AVPTNRTCRD ILRKEDENDW HSAEDIRLLT VMAALFHDIG KASQAFQAKL RNRGKPMADA YRHEWVSLRL FEAFVGPGSS DEDWLRRLAD KRETGDAWLS QLARDDRQSA PPGPFQKSRL PPLAQAVGWL IVSHHRLPNG DHRGSASLAR LPAPIQSQWC GARDADAKEK AACWQFPHGL PFASAHWRAR TALCAQSMLE RPGLLARGPA LLHDSYVMHV SRLILMLADH HYSSLPADSR LGDPNFPLHA NTDRDSGKLK QRLDEHLLGV ALHSRKLAGT LPRLERQLPR LARHKGFTRR VEQPRFRWQD KAYDCAMACR EQAMEHGFFG LNLASTGCGK TLANGRILYA LADPQRGARF SIALGLRSLT LQTGQAYRER LGLGDDDLAI LVGGSAAREL FEKQQERLER SGSESAQELL AENSHVHFAG TLEDGPLREW LGRNSAGNRL LQAPILACTI DHLMPASESL RGGHQIAPLL RLMTSDLVLD EVDDFDIDDL PALSRLVHWA GLFGSRVLLS SATLPPALVQ GLFEAYRSGR EIFQRHRGAP GRATEIRCAW FDEFSSQSSA HGAVTSFSEA HATFVAQRLA KLEQLPPRRQ AQLCTVHAAG EARPALCREL AGQMNTWMAD LHRCHHTEHQ GRRISFGLLR LANIEPLIEL AQAILAQGAP EGLHVHLCVY HSRHPLLVRS AIERQLDELL KRSDDDAAAL FARPTLAKAL QASTERDHLF VVLASPVAEV GRDHDYDWAI VEPSSMRSII QLAGRIRRHR SGFSGEANLY LLSRNIRSLE GQNPAFQRPG FETPDFPLDS HDLHDLLDPA LLARIDASPR IVEPFPLFPR SRLVDLEHRR LRALMLADDP PSSLLGVPLW WQTPASLSGA LQTSQPFRAG AKERCYALLP DEDDEERLHF SRYEEGTWSN QDNLLRNLDL TYGPRIQTWG TVNYREELVA MAGREDLDLR QCAMRYGEVR LRENTQGWSY HPYLGFKKYN |
-Macromolecule #2: anti-CRISPR protein 3 (AcrF3)
Macromolecule | Name: anti-CRISPR protein 3 (AcrF3) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD5 (virus) |
Recombinant expression | Organism: Escherichia Coli BL21(DE3) (bacteria) |
Sequence | String: MSNTISDRIV ARSVIEAARF IQSWEDADPD SLTEDQVLAA AGFAARLHEG LQATVLQRLV DESNHEEYRE FKAWEEALLN ADGRVASSPF ADWGWWYRIA NVMLATASQN VGVTWGSRVH GRLMAIFQDK FKQRYEEQA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: GiG-322 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 16 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 8.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND3 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 78480 |
-Atomic model buiding 1
Refinement | Protocol: BACKBONE TRACE |
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Output model | PDB-5gqh: |