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- PDB-7f45: Structure of an Anti-CRISPR protein -

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Basic information

Entry
Database: PDB / ID: 7f45
TitleStructure of an Anti-CRISPR protein
ComponentsAcrIF5
KeywordsIMMUNE SYSTEM / monomer / mixed alpha-beta structure
Function / homology:
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsFeng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31822012 China
CitationJournal: Nat Chem Biol / Year: 2022
Title: AcrIF5 specifically targets DNA-bound CRISPR-Cas surveillance complex for inhibition.
Authors: Yongchao Xie / Laixing Zhang / Zhengyu Gao / Peipei Yin / Hao Wang / Hang Li / Zeliang Chen / Yi Zhang / Maojun Yang / Yue Feng /
Abstract: CRISPR-Cas systems are prokaryotic antiviral systems, and phages use anti-CRISPR proteins (Acrs) to inactivate these systems. Here we present structural and functional analyses of AcrIF5, exploring ...CRISPR-Cas systems are prokaryotic antiviral systems, and phages use anti-CRISPR proteins (Acrs) to inactivate these systems. Here we present structural and functional analyses of AcrIF5, exploring its unique anti-CRISPR mechanism. AcrIF5 shows binding specificity only for the target DNA-bound form of the crRNA-guided surveillance (Csy) complex, but not the apo Csy complex from the type I-F CRISPR-Cas system. We solved the structure of the Csy-dsDNA-AcrIF5 complex, revealing that the conformational changes of the Csy complex caused by dsDNA binding dictate the binding specificity for the Csy-dsDNA complex by AcrIF5. Mechanistically, five AcrIF5 molecules bind one Csy-dsDNA complex, which destabilizes the helical bundle domain of Cas8f, thus preventing subsequent Cas2/3 recruitment. AcrIF5 exists in symbiosis with AcrIF3, which blocks Cas2/3 recruitment. This attack on the recruitment event stands in contrast to the conventional mechanisms of blocking binding of target DNA. Overall, our study reveals an unprecedented mechanism of CRISPR-Cas inhibition by AcrIF5.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 8, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcrIF5
P: AcrIF5


Theoretical massNumber of molelcules
Total (without water)17,0642
Polymers17,0642
Non-polymers00
Water00
1
A: AcrIF5


Theoretical massNumber of molelcules
Total (without water)8,5321
Polymers8,5321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: AcrIF5


Theoretical massNumber of molelcules
Total (without water)8,5321
Polymers8,5321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.741, 66.741, 120.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 45 or (resid 46...
21(chain P and (resid 3 through 32 or (resid 33...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGALAALA(chain A and (resid 3 through 45 or (resid 46...AA3 - 453 - 45
12LYSLYSALAALA(chain A and (resid 3 through 45 or (resid 46...AA46 - 4746 - 47
13ARGARGMETMET(chain A and (resid 3 through 45 or (resid 46...AA3 - 793 - 79
14ARGARGMETMET(chain A and (resid 3 through 45 or (resid 46...AA3 - 793 - 79
15ARGARGMETMET(chain A and (resid 3 through 45 or (resid 46...AA3 - 793 - 79
16ARGARGMETMET(chain A and (resid 3 through 45 or (resid 46...AA3 - 793 - 79
21ARGARGGLYGLY(chain P and (resid 3 through 32 or (resid 33...PB3 - 323 - 32
22ARGARGALAALA(chain P and (resid 3 through 32 or (resid 33...PB33 - 3633 - 36
23ARGARGVALVAL(chain P and (resid 3 through 32 or (resid 33...PB3 - 773 - 77
24ARGARGVALVAL(chain P and (resid 3 through 32 or (resid 33...PB3 - 773 - 77
25ARGARGVALVAL(chain P and (resid 3 through 32 or (resid 33...PB3 - 773 - 77
26ARGARGVALVAL(chain P and (resid 3 through 32 or (resid 33...PB3 - 773 - 77

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Components

#1: Protein AcrIF5


Mass: 8531.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: IPC1164_31450 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7M3A7R4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.52→43.97 Å / Num. obs: 3096 / % possible obs: 99.9 % / Redundancy: 22.9 % / CC1/2: 1 / Net I/σ(I): 8.25
Reflection shellResolution: 3.52→3.65 Å / Num. unique obs: 133 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EQG

7eqg


Resolution: 3.52→43.97 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.311 144 4.68 %
Rwork0.2551 2931 -
obs0.2574 3075 82.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.49 Å2 / Biso mean: 71.1147 Å2 / Biso min: 27.13 Å2
Refinement stepCycle: final / Resolution: 3.52→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 0 0 1107
Num. residues----152
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A446X-RAY DIFFRACTION11.772TORSIONAL
12P446X-RAY DIFFRACTION11.772TORSIONAL
LS refinement shellResolution: 3.52→3.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.311 144 -
Rwork0.2551 2931 -
all-3075 -
obs--83 %
Refinement TLS params.Method: refined / Origin x: -6.0604 Å / Origin y: -26.6438 Å / Origin z: -8.5743 Å
111213212223313233
T0.4116 Å2-0.134 Å20.0435 Å2-0.3167 Å20.028 Å2--0.3841 Å2
L4.7412 °2-1.6709 °2-1.76 °2-0.8668 °21.4278 °2--4.5297 °2
S-0.1611 Å °0.6197 Å °0.1644 Å °0.2946 Å °0.1815 Å °0.1135 Å °0.3167 Å °-0.6267 Å °-0.1251 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 79
2X-RAY DIFFRACTION1allP3 - 77

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