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- PDB-8kbd: Structure of CmTad1 complexed with cAAG -

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Basic information

Entry
Database: PDB / ID: 8kbd
TitleStructure of CmTad1 complexed with cAAG
Components
  • Thoeris anti-defense 1
  • cAAG
KeywordsVIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA complex
Function / homology: / Acb2/Tad1, hairpin domain / nucleotide binding / RNA / Thoeris anti-defense 1
Function and homology information
Biological speciesClostridioides mangenotii LM2 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsXiao, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2024
Title: Single phage proteins sequester signals from TIR and cGAS-like enzymes.
Authors: Li, D. / Xiao, Y. / Fedorova, I. / Xiong, W. / Wang, Y. / Liu, X. / Huiting, E. / Ren, J. / Gao, Z. / Zhao, X. / Cao, X. / Zhang, Y. / Bondy-Denomy, J. / Feng, Y.
History
DepositionAug 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Dec 4, 2024Group: Data collection / Database references / Category: citation / citation_author / reflns_shell
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
G: Thoeris anti-defense 1
H: Thoeris anti-defense 1
I: Thoeris anti-defense 1
J: Thoeris anti-defense 1
K: Thoeris anti-defense 1
L: Thoeris anti-defense 1
C: Thoeris anti-defense 1
D: Thoeris anti-defense 1
E: Thoeris anti-defense 1
F: Thoeris anti-defense 1
N: cAAG
O: cAAG
P: cAAG
Q: cAAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,29718
Polymers186,16716
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.719, 145.072, 149.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thoeris anti-defense 1 / CmTad1


Mass: 15194.333 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides mangenotii LM2 (bacteria)
Strain: LM2 / Gene: tad1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW61
#2: RNA chain
cAAG


Mass: 958.660 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: 4.21 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Ammonium sulfate, 10% v/v 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 52525 / % possible obs: 99.2 % / Redundancy: 5 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.097 / Rrim(I) all: 0.222 / Χ2: 1.636 / Net I/σ(I): 5.9 / Num. measured all: 264166
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.34 / Num. unique obs: 2535 / CC1/2: 0.279 / CC star: 0.66 / Rpim(I) all: 0.73 / Χ2: 1.144 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→34.76 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 2020 3.85 %
Rwork0.2018 --
obs0.2032 52437 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12883 0 2 0 12885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113171
X-RAY DIFFRACTIONf_angle_d1.36717799
X-RAY DIFFRACTIONf_dihedral_angle_d20.2151821
X-RAY DIFFRACTIONf_chiral_restr0.071881
X-RAY DIFFRACTIONf_plane_restr0.0082263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.230.39191400.33313233X-RAY DIFFRACTION90
3.23-3.310.34821420.30633502X-RAY DIFFRACTION97
3.31-3.410.31211440.26653581X-RAY DIFFRACTION99
3.41-3.520.29311460.25853541X-RAY DIFFRACTION99
3.52-3.650.28351380.24683608X-RAY DIFFRACTION99
3.65-3.790.27891470.22523577X-RAY DIFFRACTION99
3.79-3.960.22171400.20423614X-RAY DIFFRACTION100
3.96-4.170.21211540.17953642X-RAY DIFFRACTION100
4.17-4.430.19151430.17343610X-RAY DIFFRACTION100
4.43-4.770.19561450.16423630X-RAY DIFFRACTION100
4.77-5.250.20881430.183665X-RAY DIFFRACTION100
5.25-6.010.25981440.19233693X-RAY DIFFRACTION100
6.01-7.560.25011510.19563705X-RAY DIFFRACTION100
7.56-34.760.19491430.17023816X-RAY DIFFRACTION98

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