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- PDB-6iuf: Crystal structure of Anti-CRISPR protein AcrVA5 -

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Basic information

Entry
Database: PDB / ID: 6iuf
TitleCrystal structure of Anti-CRISPR protein AcrVA5
Componentsprotein-a
KeywordsIMMUNE SYSTEM / enzyme
Function / homologyAcyl-CoA N-acyltransferase / ACETYL COENZYME *A / Uncharacterized protein
Function and homology information
Biological speciesMoraxella bovoculi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.052 Å
AuthorsDong, L. / Guan, X. / Zhu, Y. / Huang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31825008 China
National Natural Science Foundation of China31422014 China
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: An anti-CRISPR protein disables type V Cas12a by acetylation.
Authors: Liyong Dong / Xiaoyu Guan / Ningning Li / Fan Zhang / Yuwei Zhu / Kuan Ren / Ling Yu / Fengxia Zhou / Zhifu Han / Ning Gao / Zhiwei Huang /
Abstract: Phages use anti-CRISPR proteins to deactivate the CRISPR-Cas system. The mechanisms for the inhibition of type I and type II systems by anti-CRISPRs have been elucidated. However, it has remained ...Phages use anti-CRISPR proteins to deactivate the CRISPR-Cas system. The mechanisms for the inhibition of type I and type II systems by anti-CRISPRs have been elucidated. However, it has remained unknown how the type V CRISPR-Cas12a (Cpf1) system is inhibited by anti-CRISPRs. Here we identify the anti-CRISPR protein AcrVA5 and report the mechanisms by which it inhibits CRISPR-Cas12a. Our structural and biochemical data show that AcrVA5 functions as an acetyltransferase to modify Moraxella bovoculi (Mb) Cas12a at Lys635, a residue that is required for recognition of the protospacer-adjacent motif. The AcrVA5-mediated modification of MbCas12a results in complete loss of double-stranded DNA (dsDNA)-cleavage activity. In contrast, the Lys635Arg mutation renders MbCas12a completely insensitive to inhibition by AcrVA5. A cryo-EM structure of the AcrVA5-acetylated MbCas12a reveals that Lys635 acetylation provides sufficient steric hindrance to prevent dsDNA substrates from binding to the Cas protein. Our study reveals an unprecedented mechanism of CRISPR-Cas inhibition and suggests an evolutionary arms race between phages and bacteria.
History
DepositionNov 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein-a
B: protein-a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5715
Polymers21,8602
Non-polymers1,7113
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-9 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.422, 143.422, 143.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

21A-232-

HOH

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Components

#1: Protein protein-a


Mass: 10930.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella bovoculi (bacteria) / Gene: AAX07_09540 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U2B867
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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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: 5.62 Å3/Da / Density % sol: 78.13 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 0.1M NaAc, 2M (NH4)2SO4, pH 5.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 32118 / % possible obs: 99.9 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 52.1
Reflection shellResolution: 2.05→2.09 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.052→47.807 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.91
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.1864 2995 6.25 %
Rwork0.152 --
obs0.1541 32118 80.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.052→47.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 108 125 1758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141671
X-RAY DIFFRACTIONf_angle_d1.6832274
X-RAY DIFFRACTIONf_dihedral_angle_d8.241148
X-RAY DIFFRACTIONf_chiral_restr0.082238
X-RAY DIFFRACTIONf_plane_restr0.008287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0522-2.08590.3037880.24811319X-RAY DIFFRACTION50
2.0859-2.12190.2826930.21521392X-RAY DIFFRACTION52
2.1219-2.16040.1958920.18811388X-RAY DIFFRACTION53
2.1604-2.2020.2039940.18641402X-RAY DIFFRACTION53
2.202-2.24690.1861930.1811399X-RAY DIFFRACTION53
2.2469-2.29580.2629940.18251407X-RAY DIFFRACTION53
2.2958-2.34920.2111950.18081412X-RAY DIFFRACTION53
2.3492-2.40790.2012970.18121504X-RAY DIFFRACTION56
2.4079-2.4730.22611290.1761981X-RAY DIFFRACTION73
2.473-2.54580.26391660.17242499X-RAY DIFFRACTION95
2.5458-2.6280.20591760.17422631X-RAY DIFFRACTION99
2.628-2.72190.18011830.17372647X-RAY DIFFRACTION100
2.7219-2.83090.21481770.16722650X-RAY DIFFRACTION100
2.8309-2.95970.21071770.17732663X-RAY DIFFRACTION100
2.9597-3.11570.24321780.15512677X-RAY DIFFRACTION100
3.1157-3.31090.18041760.14662653X-RAY DIFFRACTION100
3.3109-3.56640.16461690.13992661X-RAY DIFFRACTION100
3.5664-3.92520.20541780.12352654X-RAY DIFFRACTION100
3.9252-4.49280.12871760.10922665X-RAY DIFFRACTION100
4.4928-5.6590.12471720.12312671X-RAY DIFFRACTION100
5.659-47.82030.1821920.17632654X-RAY DIFFRACTION100

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