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- EMDB-6730: Anti-CRISPR protein AcrF1 bound to Csy surveillance complex with ... -

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Basic information

Entry
Database: EMDB / ID: 6730
TitleAnti-CRISPR protein AcrF1 bound to Csy surveillance complex with 32nt spacer crRNA in binding mode B
Map dataanti-CRISPR protein AcrF1 bound to Csy surveillance complex with 32nt spacer crRNA in binding mode B
Sampleanti-CRISPR protein AcrF1 bound to Csy surveillance complex with 32nt spacer crRNA in binding mode B:
Csy1 / Csy2 / Csy3 / Csy4 / AcrF1 / nucleic-acidNucleic acid
Function / homologyCRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / Uncharacterized protein / CRISPR-associated protein Csy3
Function and homology information
SourcePseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / 4.7 Å resolution
AuthorsGao GF / Peng R / Shi Y
CitationJournal: Cell Res. / Year: 2017
Title: Alternate binding modes of anti-CRISPR viral suppressors AcrF1/2 to Csy surveillance complex revealed by cryo-EM structures.
Authors: Ruchao Peng / Ying Xu / Tengfei Zhu / Ningning Li / Jianxun Qi / Yan Chai / Min Wu / Xinzheng Zhang / Yi Shi / Peiyi Wang / Jiawei Wang / Ning Gao / George Fu Gao
DateDeposition: May 11, 2017 / Header (metadata) release: Jan 10, 2018 / Map release: Jan 10, 2018 / Last update: Jan 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6730.map.gz (map file in CCP4 format, 30119 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
196 pix
1.3 Å/pix.
= 254.8 Å
196 pix
1.3 Å/pix.
= 254.8 Å
196 pix
1.3 Å/pix.
= 254.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.027 (by author), 0.027 (movie #1):
Minimum - Maximum-0.054693516 - 0.1011732
Average (Standard dev.)0.00012896564 (0.006090557)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions196196196
Origin000
Limit195195195
Spacing196196196
CellA=B=C: 254.79999 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z254.800254.800254.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.0550.1010.000

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Supplemental data

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Sample components

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Entire anti-CRISPR protein AcrF1 bound to Csy surveillance complex with ...

EntireName: anti-CRISPR protein AcrF1 bound to Csy surveillance complex with 32nt spacer crRNA in binding mode B
Number of components: 7
MassExperimental: 400 kDa

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Component #1: protein, anti-CRISPR protein AcrF1 bound to Csy surveillance comp...

ProteinName: anti-CRISPR protein AcrF1 bound to Csy surveillance complex with 32nt spacer crRNA in binding mode B
Recombinant expression: No
MassExperimental: 400 kDa
SourceSpecies: Pseudomonas aeruginosa (bacteria)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #2: protein, Csy1

ProteinName: Csy1 / Recombinant expression: No
Source (engineered)Expression System: Pseudomonas aeruginosa (bacteria)

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Component #3: protein, Csy2

ProteinName: Csy2 / Recombinant expression: No
Source (engineered)Expression System: Pseudomonas aeruginosa (bacteria)

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Component #4: protein, Csy3

ProteinName: Csy3 / Recombinant expression: No
Source (engineered)Expression System: Pseudomonas aeruginosa (bacteria)

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Component #5: protein, Csy4

ProteinName: Csy4 / Recombinant expression: No
Source (engineered)Expression System: Pseudomonas aeruginosa (bacteria)

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Component #6: protein, AcrF1

ProteinName: AcrF1 / Recombinant expression: No
Source (engineered)Expression System: Pseudomonas aeruginosa (bacteria)

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Component #7: nucleic-acid, crRNA with 32nt spacer

Nucleic-acidName: crRNA with 32nt spacer / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CUAAGAAAUU CACGGCGGGC UUGAUAUCCG CGUCUACCUG GUUCACUGCC GUGUAGGCAG

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/ml / pH: 7.5
VitrificationCryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 33773
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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