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- PDB-8qjk: Structure of the cytoplasmic domain of csx23 from Vibrio cholera ... -

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Basic information

Entry
Database: PDB / ID: 8qjk
TitleStructure of the cytoplasmic domain of csx23 from Vibrio cholera in complex with cyclic tetra-adenylate (cA4)
Components
  • Cyclic tetraadenosine monophosphate (cA4)
  • csx23
KeywordsGENE REGULATION / DNA BINDING PROTEIN Type III CRISPR effector cA4 EPR
Function / homology: / ACETYL GROUP / RNA
Function and homology information
Biological speciesVibrio cholerae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.761 Å
AuthorsMcMahon, S.A. / McQuarrie, S. / Gloster, T.M. / Gruschow, S. / White, M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004789/1 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23.
Authors: Gruschow, S. / McQuarrie, S. / Ackermann, K. / McMahon, S. / Bode, B.E. / Gloster, T.M. / White, M.F.
History
DepositionSep 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 26, 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_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: csx23
C: Cyclic tetraadenosine monophosphate (cA4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7835
Polymers11,6722
Non-polymers1113
Water81145
1
A: csx23
C: Cyclic tetraadenosine monophosphate (cA4)
hetero molecules

A: csx23
C: Cyclic tetraadenosine monophosphate (cA4)
hetero molecules

A: csx23
C: Cyclic tetraadenosine monophosphate (cA4)
hetero molecules

A: csx23
C: Cyclic tetraadenosine monophosphate (cA4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,13120
Polymers46,6878
Non-polymers44412
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Unit cell
Length a, b, c (Å)66.425, 66.425, 42.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-201-

ACE

21A-201-

ACE

31C-101-

NA

41C-205-

HOH

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Components

#1: Protein csx23


Mass: 10399.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli)
#2: RNA chain Cyclic tetraadenosine monophosphate (cA4)


Type: Polycyclic / Class: Antiviral / Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Cyclic oligoadenylates such as c-tetraAMP were found to be novel bacterial second messengers. Antiviral in context of signalling for Type III CRISPR-Cas systems.
Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002431
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic ...CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic oligoadenylate signaling was found to be essential for the type III system against the jumbo phage.
Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2MLiS04, 0.1M NaAcetate, 42.5% peg400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.76→46.97 Å / Num. obs: 5251 / % possible obs: 89.1 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 14.3
Reflection shellResolution: 1.76→1.91 Å / Num. unique obs: 264 / CC1/2: 0.721

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.761→46.97 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.239 / SU B: 5.67 / SU ML: 0.168 / Average fsc free: 0.9336 / Average fsc work: 0.9463 / Cross valid method: FREE R-VALUE / ESU R: 0.324 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2724 218 4.152 %
Rwork0.2433 5033 -
all0.245 --
obs-5251 56.615 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.049 Å20 Å20 Å2
2--0.049 Å20 Å2
3----0.098 Å2
Refinement stepCycle: LAST / Resolution: 1.761→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms619 0 95 45 759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.012733
X-RAY DIFFRACTIONr_bond_other_d0.0420.016633
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.6811005
X-RAY DIFFRACTIONr_angle_other_deg0.9471.5661483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.951581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.408103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58210113
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.0631025
X-RAY DIFFRACTIONr_chiral_restr0.0490.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02132
X-RAY DIFFRACTIONr_nbd_refined0.1940.2140
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.2534
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2305
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1110.232
X-RAY DIFFRACTIONr_nbd_other0.1390.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1030.214
X-RAY DIFFRACTIONr_mcbond_it2.554.844329
X-RAY DIFFRACTIONr_mcbond_other2.5464.844330
X-RAY DIFFRACTIONr_mcangle_it4.3127.259407
X-RAY DIFFRACTIONr_mcangle_other4.3077.259408
X-RAY DIFFRACTIONr_scbond_it1.9344.276404
X-RAY DIFFRACTIONr_scbond_other1.9324.278405
X-RAY DIFFRACTIONr_scangle_it3.296.332598
X-RAY DIFFRACTIONr_scangle_other3.2876.334599
X-RAY DIFFRACTIONr_lrange_it6.51264.376812
X-RAY DIFFRACTIONr_lrange_other6.49463.661809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc work% reflection obs (%)WRfactor RworkFsc free
1.761-1.8060.02910.325350.3166650.8845.41350.322
1.806-1.8560.36720.379990.3796700.89115.07460.3681
1.856-1.9090.51740.3851340.3886460.89921.36220.3850.74
1.909-1.9680.375150.3241820.3286260.9231.46960.3280.915
1.968-2.0320.4390.3212270.3256030.92939.13760.2990.889
2.032-2.1040.246110.272400.2685850.95242.9060.2550.955
2.104-2.1830.208150.2912640.2875730.93748.69110.2660.974
2.183-2.2720.201100.272820.2685470.95253.38210.2510.963
2.272-2.3730.27230.2972960.2945300.94260.18870.2610.955
2.373-2.4880.149130.2843180.2775000.9466.20.2420.986
2.488-2.6220.40370.3123490.3144840.93173.55370.2990.857
2.622-2.7810.387160.3143350.3174370.93380.32040.2890.892
2.781-2.9720.43100.2873840.294310.94291.41530.2670.904
2.972-3.2090.327200.2923720.2943970.93998.74060.2780.923
3.209-3.5140.264140.263580.263720.9611000.2410.946
3.514-3.9260.233130.2253320.2253450.9741000.2170.971
3.926-4.5280.233170.1892680.1922860.97799.65030.1930.976
4.528-5.5330.3260.1822550.1862610.9781000.2030.933
5.533-7.7710.32480.2021900.2071990.97899.49750.2340.943
7.771-46.970.15240.2031130.2011180.97399.15250.2650.983

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