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- PDB-9r8s: A viral SAVED protein with ring nuclease activity subverts type I... -

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Basic information

Entry
Database: PDB / ID: 9r8s
TitleA viral SAVED protein with ring nuclease activity subverts type III CRISPR defence
ComponentsSMODS-associated and fused to various effectors domain-containing protein
KeywordsVIRAL PROTEIN / SAVED anti-CRISPR Defense
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / membrane / PHOSPHATE ION / SMODS-associated and fused to various effectors domain-containing protein
Function and homology information
Biological speciesThermocrinis Great Boiling Spring virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.79 Å
AuthorsMcMahon, S.A. / White, M.F. / Orzechowski, M. / Hoikkala, V. / Chi, H. / Gloster, T.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101018608European Union
CitationJournal: To Be Published
Title: A viral SAVED protein with ring nuclease activity degrades the CRISPR second messenger cA4
Authors: Orzechowski, M. / Hoikkala, V. / Chi, H. / McMahon, S.A. / Gloster, T.M. / White, M.F.
History
DepositionMay 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMODS-associated and fused to various effectors domain-containing protein
B: SMODS-associated and fused to various effectors domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4524
Polymers55,2622
Non-polymers1902
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-11 kcal/mol
Surface area20680 Å2
Unit cell
Length a, b, c (Å)110.614, 110.614, 113.027
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 1 - 234 / Label seq-ID: 8 - 241

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein SMODS-associated and fused to various effectors domain-containing protein


Mass: 27630.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrinis Great Boiling Spring virus
Production host: Escherichia coli (E. coli) / References: UniProt: A0A823AEM5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.71 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 1.2M sodium phosphate 0.8M potassium phosphate 0.2M lithium phosphate 0.1M CAPS pH 10.5

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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: Feb 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.79→95.93 Å / Num. obs: 75593 / % possible obs: 100 % / Redundancy: 38.9 % / CC1/2: 1 / Rmerge(I) obs: 0.115 / Net I/σ(I): 17.4
Reflection shellResolution: 1.79→1.82 Å / Rmerge(I) obs: 4.572 / Num. unique obs: 4020 / CC1/2: 0.345 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.79→95.794 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.687 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 1997 2.657 %RANDOM
Rwork0.1649 73152 --
all0.166 ---
obs-75149 99.467 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.769 Å2-0.384 Å2-0 Å2
2---0.769 Å20 Å2
3---2.493 Å2
Refinement stepCycle: LAST / Resolution: 1.79→95.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 10 204 4025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123927
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163689
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.825321
X-RAY DIFFRACTIONr_angle_other_deg0.4441.7418507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1795471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.064510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10610663
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.1210174
X-RAY DIFFRACTIONr_chiral_restr0.0660.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02919
X-RAY DIFFRACTIONr_nbd_refined0.2150.2592
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22998
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21872
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21848
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2184
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.29
X-RAY DIFFRACTIONr_nbd_other0.1810.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1160.21
X-RAY DIFFRACTIONr_mcbond_it14.5963.9891890
X-RAY DIFFRACTIONr_mcbond_other14.5873.9891890
X-RAY DIFFRACTIONr_mcangle_it19.3287.1732359
X-RAY DIFFRACTIONr_mcangle_other19.3337.1752360
X-RAY DIFFRACTIONr_scbond_it18.1964.592037
X-RAY DIFFRACTIONr_scbond_other18.1514.5922030
X-RAY DIFFRACTIONr_scangle_it24.6538.1442962
X-RAY DIFFRACTIONr_scangle_other24.6078.1452951
X-RAY DIFFRACTIONr_lrange_it27.87340.0714220
X-RAY DIFFRACTIONr_lrange_other27.82739.8834185
X-RAY DIFFRACTIONr_rigid_bond_restr3.30737616
X-RAY DIFFRACTIONr_ncsr_local_group_10.1480.057048
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.147920.05008
12BX-RAY DIFFRACTIONLocal ncs0.147920.05008
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 freeFsc work% reflection obs (%)WRfactor Rwork
1.79-1.8360.391980.39150700.39155400.8880.88593.28520.385
1.836-1.8870.4031600.35951990.3653810.8870.90699.59120.356
1.887-1.9410.2981100.3251270.3252380.9430.93599.98090.32
1.941-2.0010.2711710.26449460.26451180.9490.95999.98050.26
2.001-2.0670.2551180.2147830.21149010.9560.9731000.203
2.067-2.1390.2131140.17447080.17548230.9720.98299.97930.157
2.139-2.220.2361060.16145050.16346130.9650.98599.95660.142
2.22-2.3110.2091380.14343240.14544660.9750.98899.91040.12
2.311-2.4130.1911100.13441710.13642810.9750.991000.109
2.413-2.5310.1821420.1439510.14140930.980.991000.116
2.531-2.6680.1931140.13837650.1438790.9790.991000.112
2.668-2.8290.231140.14436140.14737280.9710.9891000.121
2.829-3.0250.233750.17533750.17634500.9620.9821000.149
3.025-3.2670.241920.17331610.17432530.9690.9841000.157
3.267-3.5780.199940.17929040.17929980.9780.9841000.166
3.578-40.19620.15626630.15627250.9850.9881000.147
4-4.6170.155790.11223390.11324180.9860.9931000.111
4.617-5.6520.138420.12820260.12820680.9880.9931000.13
5.652-7.9790.215370.17315940.17416310.9740.9871000.171
7.979-95.7940.231210.1749260.1759470.9580.9791000.197

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