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- EMDB-9535: Cryo-EM Structure of the PaeCas3-AcrF3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9535
TitleCryo-EM Structure of the PaeCas3-AcrF3 complex
Map dataCryo-EM structure of PaeCas3-AcrF3 complex
Sample
  • Complex: PaeCas3-AcrF3 complex
    • Complex: type I-F CRISPR-associated nuclease/helicase Cas3
      • Protein or peptide: type I-F CRISPR-associated nuclease/helicase Cas3
    • Complex: anti-CRISPR protein 3 (AcrF3)
      • Protein or peptide: anti-CRISPR protein 3 (AcrF3)
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
: / Cas3 inhibitor AcrF3 / Helicase Cas3, CRISPR-associated, Yersinia-type / : / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain / Cas3, HD domain / : / CRISPR-associated Cas3-type HD domain ...: / Cas3 inhibitor AcrF3 / Helicase Cas3, CRISPR-associated, Yersinia-type / : / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain / Cas3, HD domain / : / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phage protein / CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / Pseudomonas phage JBD5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsZhang X / Ma J / Wang Y / Wang J
CitationJournal: 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
DepositionAug 7, 2016-
Header (metadata) releaseSep 21, 2016-
Map releaseSep 21, 2016-
UpdateOct 19, 2016-
Current statusOct 19, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5gqh
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9535.png

Downloads & links

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Map

FileDownload / File: emd_9535.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of PaeCas3-AcrF3 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 140 pix.
= 114.8 Å		0.82 Å/pix.
x 140 pix.
= 114.8 Å		0.82 Å/pix.
x 140 pix.
= 114.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.1324326 - 0.19505402
Average (Standard dev.)0.0014116985 (±0.019745765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-70
Dimensions140140140
Spacing140140140
CellA=B=C: 114.799995 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z114.800114.800114.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-0.1320.1950.001

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Supplemental data

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Sample components

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Entire : PaeCas3-AcrF3 complex

EntireName: PaeCas3-AcrF3 complex
Components
  • Complex: PaeCas3-AcrF3 complex
    • Complex: type I-F CRISPR-associated nuclease/helicase Cas3
      • Protein or peptide: type I-F CRISPR-associated nuclease/helicase Cas3
    • Complex: anti-CRISPR protein 3 (AcrF3)
      • Protein or peptide: anti-CRISPR protein 3 (AcrF3)

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Supramolecule #1: PaeCas3-AcrF3 complex

SupramoleculeName: PaeCas3-AcrF3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 158 kDa/nm

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Supramolecule #2: type I-F CRISPR-associated nuclease/helicase Cas3

SupramoleculeName: type I-F CRISPR-associated nuclease/helicase Cas3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia Coli BL21(DE3) (bacteria) / Recombinant plasmid: pET

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Supramolecule #3: anti-CRISPR protein 3 (AcrF3)

SupramoleculeName: anti-CRISPR protein 3 (AcrF3) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Pseudomonas phage JBD5 (virus)
Recombinant expressionOrganism: Escherichia Coli BL21(DE3) (bacteria) / Recombinant plasmid: pET

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Macromolecule #1: type I-F CRISPR-associated nuclease/helicase Cas3

MacromoleculeName: type I-F CRISPR-associated nuclease/helicase Cas3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia Coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: anti-CRISPR protein 3 (AcrF3)

MacromoleculeName: anti-CRISPR protein 3 (AcrF3) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD5 (virus)
Recombinant expressionOrganism: Escherichia Coli BL21(DE3) (bacteria)
SequenceString:
MSNTISDRIV ARSVIEAARF IQSWEDADPD SLTEDQVLAA AGFAARLHEG LQATVLQRLV DESNHEEYRE FKAWEEALLN ADGRVASSPF ADWGWWYRIA NVMLATASQN VGVTWGSRVH GRLMAIFQDK FKQRYEEQA

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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
GridModel: GiG-322 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 16 K / Instrument: LEICA EM GP

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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: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND3
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4q2c

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 78480
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-5gqh:
Cryo-EM structure of PaeCas3-AcrF3 complex

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