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- EMDB-64090: AcrIE10-Cas7-IR complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64090
TitleAcrIE10-Cas7-IR complex
Map dataAcrIE10-Cas7-IR complex map
Sample
  • Complex: AcrIE10-Cas7*-IR complex
    • DNA: DNA (5'-D(P*TP*GP*TP*AP*TP*GP*AP*CP*AP*TP*CP*TP*GP*TP*CP*AP*TP*AP*C)-3')
    • DNA: DNA (5'-D(P*GP*TP*AP*TP*GP*AP*CP*AP*GP*AP*TP*GP*TP*CP*AP*TP*AP*CP*AP*A)-3')
    • Protein or peptide: AcrIE10
    • Protein or peptide: CRISPR-associated protein Cse4
KeywordsAnti-CRISPR / Transcription inhibitor / TRANSCRIPTION
Function / homologyCRISPR-associated protein, CT1975 / CT1975-like protein / Uncharacterized protein / CRISPR-associated protein Cse4
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsTsui WT / Ma JB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of AcrIE10-Cas7-IR complex
Authors: Tsui WT / Ma JB
History
DepositionApr 9, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64090.png

Downloads & links

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Map

FileDownload / File: emd_64090.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcrIE10-Cas7-IR complex map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 180 pix.
= 172.8 Å		0.96 Å/pix.
x 180 pix.
= 172.8 Å		0.96 Å/pix.
x 180 pix.
= 172.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.119
Minimum - Maximum-0.5461344 - 0.8528598
Average (Standard dev.)0.0035821514 (±0.029437503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 172.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64090_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_64090_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 : AcrIE10-Cas7*-IR complex

EntireName: AcrIE10-Cas7*-IR complex
Components
  • Complex: AcrIE10-Cas7*-IR complex
    • DNA: DNA (5'-D(P*TP*GP*TP*AP*TP*GP*AP*CP*AP*TP*CP*TP*GP*TP*CP*AP*TP*AP*C)-3')
    • DNA: DNA (5'-D(P*GP*TP*AP*TP*GP*AP*CP*AP*GP*AP*TP*GP*TP*CP*AP*TP*AP*CP*AP*A)-3')
    • Protein or peptide: AcrIE10
    • Protein or peptide: CRISPR-associated protein Cse4

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Supramolecule #1: AcrIE10-Cas7*-IR complex

SupramoleculeName: AcrIE10-Cas7*-IR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cas7* binds to AcrIE10-IR complex
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: DNA (5'-D(P*TP*GP*TP*AP*TP*GP*AP*CP*AP*TP*CP*TP*GP*TP*CP*AP*TP*AP...

MacromoleculeName: DNA (5'-D(P*TP*GP*TP*AP*TP*GP*AP*CP*AP*TP*CP*TP*GP*TP*CP*AP*TP*AP*C)-3')
type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 5.794771 KDa
SequenceString:
(DT)(DG)(DT)(DA)(DT)(DG)(DA)(DC)(DA)(DT) (DC)(DT)(DG)(DT)(DC)(DA)(DT)(DA)(DC)

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Macromolecule #2: DNA (5'-D(P*GP*TP*AP*TP*GP*AP*CP*AP*GP*AP*TP*GP*TP*CP*AP*TP*AP*CP...

MacromoleculeName: DNA (5'-D(P*GP*TP*AP*TP*GP*AP*CP*AP*GP*AP*TP*GP*TP*CP*AP*TP*AP*CP*AP*A)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 6.16603 KDa
SequenceString:
(DG)(DT)(DA)(DT)(DG)(DA)(DC)(DA)(DG)(DA) (DT)(DG)(DT)(DC)(DA)(DT)(DA)(DC)(DA)(DA)

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Macromolecule #3: AcrIE10

MacromoleculeName: AcrIE10 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 13.185825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VKKEISRNPS FTPSPKLRAH LNSHREGVTE RLNNIFDRYA HLVRACALPL DDDETQVLLN VLNGSVVEPA FIEYLAQEIR DSDDYLEGI PAAKSLYEKC QSATYPQLLA TVERLDR

UniProtKB: Uncharacterized protein

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Macromolecule #4: CRISPR-associated protein Cse4

MacromoleculeName: CRISPR-associated protein Cse4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 38.323203 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTFIQLHLL TAYPAANLNR DDTGAPKTVM LGGATRLRIS SQSLKRAWRT SELFEHALAG HIGIRSGRIA REAAEILVKS GIEPRKAVD YVKAIGECFG KVKTKADQND PLKCSETEQL AHISPAEFDA VKALAHRLAE EKRAATKEEA ALLRHDRMAV D IAMFGRML ...String:
MTTFIQLHLL TAYPAANLNR DDTGAPKTVM LGGATRLRIS SQSLKRAWRT SELFEHALAG HIGIRSGRIA REAAEILVKS GIEPRKAVD YVKAIGECFG KVKTKADQND PLKCSETEQL AHISPAEFDA VKALAHRLAE EKRAATKEEA ALLRHDRMAV D IAMFGRML ADQPTYNVEA ACQVAHAFGV SETIVEDDFF TAVDDLRAAS EDAGAGHLGE TGFGSALFYT YICIDKDLLV NN LNGNEEL ANKTLRAFTE AALKVSPTGK QNSFASRAYA SWALAEKGTD QPRSLAAAFY QPINGGDQLD VAVQRITALR ENM NTVYGQ QTAFQHFDVM NKQGSMNDVL DFICA

UniProtKB: CRISPR-associated protein Cse4

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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: 7.8 / Details: 20mM Tris-HCl, 150mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 1.2 sec. / 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: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108754
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9uer:
AcrIE10-Cas7-IR complex

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