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- PDB-8k0k: Crystal structure of Csy complex -

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Basic information

Entry
Database: PDB / ID: 8k0k
TitleCrystal structure of Csy complex
Components
  • Csy1
  • Csy2
  • Csy3
  • Csy4
  • RNA (60-MER)
KeywordsRNA BINDING PROTEIN/RNA / complex / RNA-protein complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity
Similarity search - Function
CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3)
Similarity search - Domain/homology
RNA / RNA (> 10) / Csy3 / Csy2 / Csy1 / Csy4
Similarity search - Component
Biological speciesVibrio phage ICP1_2011_A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.995 Å
AuthorsFeng, Y. / Wang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: Nat Chem Biol / Year: 2024
Title: Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system.
Authors: Laixing Zhang / Hao Wang / Jianwei Zeng / Xueli Cao / Zhengyu Gao / Zihe Liu / Feixue Li / Jiawei Wang / Yi Zhang / Maojun Yang / Yue Feng /
Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are prokaryotic adaptive immune systems against invading phages and other mobile genetic elements. Notably, some phages, ...Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are prokaryotic adaptive immune systems against invading phages and other mobile genetic elements. Notably, some phages, including the Vibrio cholerae-infecting ICP1 (International Center for Diarrheal Disease Research, Bangladesh cholera phage 1), harbor CRISPR-Cas systems to counteract host defenses. Nevertheless, ICP1 Cas8f lacks the helical bundle domain essential for recruitment of helicase-nuclease Cas2/3 during target DNA cleavage and how this system accomplishes the interference stage remains unknown. Here, we found that Cas1, a highly conserved component known to exclusively work in the adaptation stage, also mediates the interference stage through connecting Cas2/3 to the DNA-bound CRISPR-associated complex for antiviral defense (Cascade; CRISPR system yersinia, Csy) of the ICP1 CRISPR-Cas system. A series of structures of Csy, Csy-dsDNA (double-stranded DNA), Cas1-Cas2/3 and Csy-dsDNA-Cas1-Cas2/3 complexes reveal the whole process of Cas1-mediated target DNA cleavage by the ICP1 CRISPR-Cas system. Together, these data support an unprecedented model in which Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system and the study also sheds light on a unique model of primed adaptation.
History
DepositionJul 9, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Csy1
B: Csy2
C: Csy3
D: Csy3
E: Csy3
F: Csy3
G: Csy3
H: Csy3
I: Csy4
J: RNA (60-MER)


Theoretical massNumber of molelcules
Total (without water)285,99010
Polymers285,99010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43720 Å2
ΔGint-198 kcal/mol
Surface area98640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.853, 95.077, 204.031
Angle α, β, γ (deg.)90.00, 93.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Csy1 / Cas8f


Mass: 20409.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2011_A (virus) / Gene: csy1, ICP12011A_088 / Production host: Escherichia coli (E. coli) / References: UniProt: M1R2X3
#2: Protein Csy2 / Cas5f


Mass: 27401.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2011_A (virus) / Gene: csy2, ICP12011A_087 / Production host: Escherichia coli (E. coli) / References: UniProt: M1QWL5
#3: Protein
Csy3 / Cas7f


Mass: 33399.301 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2011_A (virus) / Gene: csy3, ICP12011A_086 / Production host: Escherichia coli (E. coli) / References: UniProt: M1Q7R8
#4: Protein Csy4 / Cas6f


Mass: 18736.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2011_A (virus) / Gene: csy4, ICP12011A_085 / Production host: Escherichia coli (E. coli) / References: UniProt: M1R9H3
#5: RNA chain RNA (60-MER)


Mass: 19046.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2011_A (virus) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: 4.04 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.995→50 Å / Num. obs: 85253 / % possible obs: 97.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 14.9
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.912 / Num. unique obs: 6128

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.995→46.295 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.74 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 4257 5 %
Rwork0.198 --
obs0.2 85208 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.995→46.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18474 1260 0 0 19734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320204
X-RAY DIFFRACTIONf_angle_d0.6527663
X-RAY DIFFRACTIONf_dihedral_angle_d15.94211845
X-RAY DIFFRACTIONf_chiral_restr0.0453205
X-RAY DIFFRACTIONf_plane_restr0.0043380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9954-3.02940.3405890.2861424X-RAY DIFFRACTION51
3.0294-3.0650.32051220.27592179X-RAY DIFFRACTION74
3.065-3.10240.33491200.2732194X-RAY DIFFRACTION77
3.1024-3.14170.31091240.27342330X-RAY DIFFRACTION79
3.1417-3.1830.34041260.26272429X-RAY DIFFRACTION84
3.183-3.22660.31291070.26882413X-RAY DIFFRACTION82
3.2266-3.27270.27131060.25462371X-RAY DIFFRACTION80
3.2727-3.32150.29211500.24492608X-RAY DIFFRACTION90
3.3215-3.37340.29721500.25642773X-RAY DIFFRACTION96
3.3734-3.42870.27061490.24532802X-RAY DIFFRACTION98
3.4287-3.48780.30871450.23822874X-RAY DIFFRACTION98
3.4878-3.55120.28771540.23132840X-RAY DIFFRACTION98
3.5512-3.61950.2461830.22752880X-RAY DIFFRACTION99
3.6195-3.69330.28721490.22492879X-RAY DIFFRACTION99
3.6933-3.77360.24211390.22872907X-RAY DIFFRACTION99
3.7736-3.86130.26431850.21222831X-RAY DIFFRACTION99
3.8613-3.95780.24341360.20692902X-RAY DIFFRACTION99
3.9578-4.06480.23941420.18932855X-RAY DIFFRACTION98
4.0648-4.18430.21131500.18672905X-RAY DIFFRACTION99
4.1843-4.31930.24871510.18192911X-RAY DIFFRACTION99
4.3193-4.47350.20061240.16982864X-RAY DIFFRACTION99
4.4735-4.65250.18391440.16372858X-RAY DIFFRACTION97
4.6525-4.8640.20291250.16382572X-RAY DIFFRACTION88
4.864-5.12010.20851650.16872927X-RAY DIFFRACTION99
5.1201-5.44050.18531520.17272908X-RAY DIFFRACTION100
5.4405-5.85980.21461780.1722925X-RAY DIFFRACTION100
5.8598-6.44810.22041580.17862932X-RAY DIFFRACTION100
6.4481-7.37790.20281470.17382929X-RAY DIFFRACTION99
7.3779-9.28310.19471510.15372855X-RAY DIFFRACTION96
9.2831-46.2950.21441360.17082874X-RAY DIFFRACTION94

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