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- EMDB-61698: crRNA-guided surveillance (Csy) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61698
TitlecrRNA-guided surveillance (Csy) complex
Map data
Sample
  • Complex: Cys complex
    • Protein or peptide: Type I-F CRISPR-associated protein Csy1
    • Protein or peptide: Type I-F CRISPR-associated protein Csy2
    • Protein or peptide: Type I-F CRISPR-associated protein Csy3
    • RNA: RNA (49-MER)
Keywordscomplex / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
Function / homologyCRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / Type I-F CRISPR-associated protein Csy1 / Type I-F CRISPR-associated protein Csy2 / Type I-F CRISPR-associated protein Csy3
Function and homology information
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang WH / Guan LL / Du XY / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000901 China
CitationJournal: To Be Published
Title: crRNA-guided surveillance (Csy) complex
Authors: Wang WH / Guan LL / Du XY / Feng Y
History
DepositionSep 26, 2024-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61698.png

Downloads & links

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Map

FileDownload / File: emd_61698.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 267.968 Å		0.84 Å/pix.
x 320 pix.
= 267.968 Å		0.84 Å/pix.
x 320 pix.
= 267.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8374 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.8406092 - 2.426733
Average (Standard dev.)-0.0006310027 (±0.05707398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.96802 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61698_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61698_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61698_half_map_2.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 : Cys complex

EntireName: Cys complex
Components
  • Complex: Cys complex
    • Protein or peptide: Type I-F CRISPR-associated protein Csy1
    • Protein or peptide: Type I-F CRISPR-associated protein Csy2
    • Protein or peptide: Type I-F CRISPR-associated protein Csy3
    • RNA: RNA (49-MER)

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Supramolecule #1: Cys complex

SupramoleculeName: Cys complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)

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Macromolecule #1: Type I-F CRISPR-associated protein Csy1

MacromoleculeName: Type I-F CRISPR-associated protein Csy1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 53.641059 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SSGLVDYKDD DDKDYKDDDD KHGSHMASVS TGPNGEFSSP TLRQLIESFI QERLQGKLDK LKPDEDDKRQ ALLAGHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAPG QPGLAGSHEL ADELVSDVVG NAAALDVFKF L SLQYQGRY ...String:
MGSSHHHHHH SSGLVDYKDD DDKDYKDDDD KHGSHMASVS TGPNGEFSSP TLRQLIESFI QERLQGKLDK LKPDEDDKRQ ALLAGHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAPG QPGLAGSHEL ADELVSDVVG NAAALDVFKF L SLQYQGRY LLNWLTENSA EALQALSDDP EQAREWRQAF VGITAGKAAP ASHSLAKQLY FPLPGSGYHL LAPLFPTSLV QR VHGQIRE ARFGEAARAA REARQQKKPW PHGFSEYPNL AIQKFGGTKP QNISQLNSER HGENWLLASL PPHWEPQELR APL QQVSVF EHDLGRSPEV ARLTRTLRGF LATTKHNNLA IRQHRAQLVG QICDEALHYA ARLRELEPGW SASSDCRLHE AEQL WLDPL RVHTDEAFMR RRLWGDWPME VSERFANWLN RALTNKGLVM GEAESRQWRK DLGKELKMFK EILEDERD

UniProtKB: Type I-F CRISPR-associated protein Csy1

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Macromolecule #2: Type I-F CRISPR-associated protein Csy2

MacromoleculeName: Type I-F CRISPR-associated protein Csy2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 36.093863 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF AHALQRRIGA TLDIELDGVG IICHRFEAQV SQPAGKHTLV FNLSRNPLN RDGSTAAIVE EGRAHLEVSL LLGVRGDGLD DHPAQEIARQ VQEQASAMRL AGGSILPRCN ERCPAPSAEL L MLGGSDEQ ...String:
MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF AHALQRRIGA TLDIELDGVG IICHRFEAQV SQPAGKHTLV FNLSRNPLN RDGSTAAIVE EGRAHLEVSL LLGVRGDGLD DHPAQEIARQ VQEQASAMRL AGGSILPRCN ERCPAPSAEL L MLGGSDEQ RRKNQRRLTR RLLPGFALVS REAMLQQHLE DLRSTTPEAT TLDALLDLSR LNFEPPATSP AEAASPLEAS WQ VRDKPGW LVPIPAGYNA LSPLYAPGEV RNARDRETPL RFVENLFSLG QWISPHRVTV LQDLLWYHQV EPDDGIYRWS TPR FAKHAI A

UniProtKB: Type I-F CRISPR-associated protein Csy2

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Macromolecule #3: Type I-F CRISPR-associated protein Csy3

MacromoleculeName: Type I-F CRISPR-associated protein Csy3 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 37.534148 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSKQTLNTAS VLAFERKLDP SDALLSAGDW AQRDASQQWP AVSVIAKSVR GTISNRLKTK DRDPAKLDAS IQSPNLQTVD VANLPSDAD TLKVRFTLRV LGGAGTPSAC NDAAYRDKLL QTVATYVNDQ GFAELARRYA HNLANARFLW RNRVGAEAVE V RINHIRQG ...String:
MSKQTLNTAS VLAFERKLDP SDALLSAGDW AQRDASQQWP AVSVIAKSVR GTISNRLKTK DRDPAKLDAS IQSPNLQTVD VANLPSDAD TLKVRFTLRV LGGAGTPSAC NDAAYRDKLL QTVATYVNDQ GFAELARRYA HNLANARFLW RNRVGAEAVE V RINHIRQG EVARAWRFDA LAIGLRDFKA DAELDALAEL IASGLSGSGH VLLEVVAFAR IGDGQEVFPS QELILDKGDK KG QKSKTLY SVRDAAAIHS QKIGNALRTI DTWYPDEDGL GPIAVEPYGS VTSQGKAYRQ PKQKLDFYTL LDNWVLRDEA PAV EQQHYV IANLIRGGVF GEAEEK

UniProtKB: Type I-F CRISPR-associated protein Csy3

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Macromolecule #4: RNA (49-MER)

MacromoleculeName: RNA (49-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 15.736397 KDa
SequenceString:
CUAAGAAAUA GUGCAGCUUC UUAUGAUGCG CCCACUGCCG AAUAGGCAG

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: OTHER / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146897
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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