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- EMDB-34524: Cryo-EM structure of Synechocystis sp. PCC6714 Cascade at 3.8 ang... -

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Basic information

Entry
Database: EMDB / ID: EMD-34524
TitleCryo-EM structure of Synechocystis sp. PCC6714 Cascade at 3.8 angstrom resolution
Map data
Sample
  • Complex: Type I-B Cascade
    • RNA: CRISPR RNA
    • DNA: Target DNA
    • DNA: Non target DNA
    • Protein or peptide: CRISPR associated protein Cas5
    • Protein or peptide: CRISPR associated protein Cas8
    • Protein or peptide: CRISPR associated protein Cas11b
KeywordsType I-B / CRISPR-Cas / Cascade / RNA BINDING PROTEIN
Function / homology
Function and homology information


defense response to virus
Similarity search - Function
CRISPR type MYXAN-associated protein Cmx8 / : / : / Type I-B CRISPR Cas8b N-terminal domain / Type I-B CRISPR Cas8b C-terminal domain / CRISPR-associated protein Cas5, N-terminal
Similarity search - Domain/homology
Uncharacterized protein / Fruiting body developmental protein R-like protein / Type I-MYXAN CRISPR-associated protein Cmx8
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6714 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXiao Y / Lu M / Yu C / Zhang Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970547 China
Ministry of Science and Technology (MoST, China)2018YFA0902000 China
CitationJournal: To Be Published
Title: Cryo-EM structure of Synechocystis sp. PCC6714 Cascade at 3.8 angstrom resolution
Authors: Xiao Y / Lu M / Yu C / Zhang Y
History
DepositionOct 20, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34524.png

Downloads & links

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Map

FileDownload / File: emd_34524.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 280 pix.
= 385. Å		1.38 Å/pix.
x 280 pix.
= 385. Å		1.38 Å/pix.
x 280 pix.
= 385. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.5963646 - 1.6645005
Average (Standard dev.)0.00042726065 (±0.057397738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 385.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34524_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34524_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 : Type I-B Cascade

EntireName: Type I-B Cascade
Components
  • Complex: Type I-B Cascade
    • RNA: CRISPR RNA
    • DNA: Target DNA
    • DNA: Non target DNA
    • Protein or peptide: CRISPR associated protein Cas5
    • Protein or peptide: CRISPR associated protein Cas8
    • Protein or peptide: CRISPR associated protein Cas11b

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Supramolecule #1: Type I-B Cascade

SupramoleculeName: Type I-B Cascade / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #6, #4-#5
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)

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Macromolecule #1: CRISPR RNA

MacromoleculeName: CRISPR RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.380655 KDa
SequenceString:
UUUAUCACCG UGUCCCCAAU CUGGAUAUUU UGUGUG

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Macromolecule #2: Target DNA

MacromoleculeName: Target DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.847038 KDa
SequenceString:
(DA)(DC)(DA)(DC)(DA)(DA)(DA)(DA)(DT)(DA) (DT)(DC)(DC)(DA)(DG)(DA)(DT)(DT)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DC)(DG)(DG)(DT) (DG)(DA)(DT)(DA)(DA)(DA)

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Macromolecule #3: Non target DNA

MacromoleculeName: Non target DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.42226 KDa
SequenceString:
(DC)(DA)(DT)(DG)(DT)(DG)(DG)(DG)(DA)(DA) (DA)

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Macromolecule #4: CRISPR associated protein Cas8

MacromoleculeName: CRISPR associated protein Cas8 / type: protein_or_peptide / ID: 4 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria) / Strain: PCC 6714
Molecular weightTheoretical: 33.789074 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSNLNLFATI LTYPAPASNY RGESEENRSV IQKILKDGQK YAIISPESMR NALREMLIEL GQPNNRTRLH SEDQLAVEFK EYPNPDKFA DDFLFGYMVA QTNDAKEMKK LNRPAKRDSI FRCNMAVAVN PYKYDTVFYQ SPLNAGDSAW KNSTSSALLH R EVTHTAFQ ...String:
MSNLNLFATI LTYPAPASNY RGESEENRSV IQKILKDGQK YAIISPESMR NALREMLIEL GQPNNRTRLH SEDQLAVEFK EYPNPDKFA DDFLFGYMVA QTNDAKEMKK LNRPAKRDSI FRCNMAVAVN PYKYDTVFYQ SPLNAGDSAW KNSTSSALLH R EVTHTAFQ YPFALAGKDC AAKPEWVKAL LQAIAELNGV AGGHARAYYE FAPRSVVARL TPKLVAGYQT YGFDAEGNWL EL SRLTATD SDNLDLPANE FWLGGELVRK MDQEQKAQLE AMGAHLYANP EKLFADLADS FLGV

UniProtKB: Fruiting body developmental protein R-like protein

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Macromolecule #5: CRISPR associated protein Cas11b

MacromoleculeName: CRISPR associated protein Cas11b / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria) / Strain: PCC 6714
Molecular weightTheoretical: 14.5385 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MTVATTKTRE YAEIVYKIAQ GFVLSKLSSK HDLQWSKCKG NPKLEREYND KKEKVVNEAF LAIRSRTEKQ AFIDYFVSTL YPHVRQDEF VDFAQKLFQD TDEIRSLTLL ALSSQYPIKR QGETE

UniProtKB: Type I-MYXAN CRISPR-associated protein Cmx8

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Macromolecule #6: CRISPR associated protein Cas5

MacromoleculeName: CRISPR associated protein Cas5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria) / Strain: PCC 6714
Molecular weightTheoretical: 26.592424 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAQLALALDT VTRYLRLKAP FAAFRPFQSG SFRSTTPVPS FSAVYGLLLN LAGIEQRQEV EGKVTLIKPK AELPKLAIAI GQVKPSSTS LINQQLHNYP VGNSGKEFAS RTFGSKYWIA PVRREVLVNL DLIIGLQSPV EFWQKLDQGL KGETVINRYG L PFAGDNNF ...String:
MAQLALALDT VTRYLRLKAP FAAFRPFQSG SFRSTTPVPS FSAVYGLLLN LAGIEQRQEV EGKVTLIKPK AELPKLAIAI GQVKPSSTS LINQQLHNYP VGNSGKEFAS RTFGSKYWIA PVRREVLVNL DLIIGLQSPV EFWQKLDQGL KGETVINRYG L PFAGDNNF LFDEIYPIEK PDLASWYCPL EPDTRPNQGA CRLTLWIDRE NNTQTTIKVF SPSDFRLEPP AKAWQQLPG

UniProtKB: Uncharacterized protein

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 175158
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER

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