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- PDB-5xlp: Anti-CRISPR proteins AcrF1/2 bound to Csy surveillance complex wi... -

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Database: PDB / ID: 5xlp
TitleAnti-CRISPR proteins AcrF1/2 bound to Csy surveillance complex with a 20nt spacer crRNA backbone region
  • CRISPR-associated protein Csy3
  • Uncharacterized protein AcrF1
  • crRNA with 20nt spacer sequence
KeywordsIMMUNE SYSTEM/RNA / anti-CRISPR proteins / Csy complex / Type I-F CRISPR/Cas system / IMMUNE SYSTEM-RNA complex
Function / homologyCRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / Uncharacterized protein / CRISPR-associated protein Csy3
Function and homology information
Specimen sourcePseudomonas aeruginosa (bacteria)
Pseudomonas phage JBD30 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsPeng, R. / Shi, Y. / Gao, G.F.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 11, 2017 / Release: Jan 10, 2018

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Deposited unit
C: CRISPR-associated protein Csy3
D: CRISPR-associated protein Csy3
E: CRISPR-associated protein Csy3
F: CRISPR-associated protein Csy3
K: crRNA with 20nt spacer sequence
M: Uncharacterized protein AcrF1

Theoretical massNumber of molelcules
Total (without water)174,5986

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)18050
ΔGint (kcal/M)-113
Surface area (Å2)64960


#1: Protein/peptide
CRISPR-associated protein Csy3

Mass: 37579.273 Da / Num. of mol.: 4
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: csy3, csy1-3, PA14_33310
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q02MM1
#2: RNA chain crRNA with 20nt spacer sequence

Mass: 15456.173 Da / Num. of mol.: 1 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
#3: Protein/peptide Uncharacterized protein AcrF1

Mass: 8824.931 Da / Num. of mol.: 1
Source: (gene. exp.) Pseudomonas phage JBD30 (bacteriophage)
Gene: JBD30_035
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: L7P7M1

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

IDNameTypeEntity IDParent IDSource
1anti-CRISPR proteins AcrF1/2 bound to Csy surveillance complex with a 20nt spacer sequence backbone regionCOMPLEX1, 2, 30RECOMBINANT
2man CRISPR-associated protein Csy3COMPLEX11RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: YES
Source (natural)
IDEntity assembly IDNcbi tax IDOrganismStrain
21208963Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)UCBPP-PA14
31287Pseudomonas aeruginosa (bacteria)
411223260Pseudomonas phage D30
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
21866768Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
31866768Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
41866768Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingAverage exposure time: 0.35 sec. / Electron dose: 1.55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 38


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
1RELION2.0particle selection
4CTF3.0CTF correction
7Chimera2015-04-15model fitting
9RELION2.0initial Euler assignment
10RELION2.0final Euler assignment
12RELION2.03D reconstruction
13PHENIX1.11model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 154095 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00910142
ELECTRON MICROSCOPYf_angle_d1.35613963
ELECTRON MICROSCOPYf_dihedral_angle_d13.2805999
ELECTRON MICROSCOPYf_chiral_restr0.0641691
ELECTRON MICROSCOPYf_plane_restr0.0091783

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