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- PDB-9iad: Chroococcidiopsis thermalis Argonaute (CtAgo) bound to the 3' end... -

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Basic information

Entry
Database: PDB / ID: 9iad
TitleChroococcidiopsis thermalis Argonaute (CtAgo) bound to the 3' end of a guide DNA
Components
  • DNA (5'-D(P*TP*TP*GP*T)-3')
  • Protein argonaute
KeywordsIMMUNE SYSTEM / Prokaryotic Argonaute / deoxyribonuclease / hydrolase / slicer
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
Piwi domain profile. / Piwi domain / Piwi domain / Piwi / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesChroococcidiopsis thermalis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBobadilla Ugarte, P. / Swarts, D.C.
Funding supportEuropean Union, Netherlands, Mexico, 3items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2020-STG 948783European Union
Netherlands Organisation for Scientific Research (NWO)016.Veni.192.072 Netherlands
Consejo Nacional de Ciencia y Tecnologia (CONACYT)682509 Mexico
CitationJournal: Mol.Cell / Year: 2025
Title: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA.
Authors: Bobadilla Ugarte, P. / Halter, S. / Mutte, S.K. / Heijstek, C. / Niault, T. / Terenin, I. / Barendse, P. / Koopal, B. / Roosjen, M. / Boeren, S. / Hauryliuk, V. / Jinek, M. / Westphal, A.H. / Swarts, D.C.
History
DepositionFeb 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 28, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein argonaute
B: DNA (5'-D(P*TP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)89,8992
Polymers89,8992
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-3 kcal/mol
Surface area32590 Å2
Unit cell
Length a, b, c (Å)74.901, 50.590, 98.572
Angle α, β, γ (deg.)90.000, 102.750, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Protein argonaute


Mass: 84874.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein was expressed with N-terminal His-MBP-TEV tag, hence amino acids 1 and 2 (SA) are different than wildtype sequence (M)
Source: (gene. exp.) Chroococcidiopsis thermalis (bacteria) / Gene: Chro_5199 / Production host: Escherichia coli (E. coli) / References: UniProt: K9U8J6
#2: DNA chain DNA (5'-D(P*TP*TP*GP*T)-3')


Mass: 5024.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution: -3.74 mg/ml CtAgo -500 mM KCl -20 mM HEPES-KOH pH7.5 -1 mM DTT Reservoir solution: -0.05 M Ammonium Formate -8% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.4→48.07 Å / Num. obs: 28341 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 63.08 Å2 / CC1/2: 1 / Rrim(I) all: 0.085 / Net I/σ(I): 12.06
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 0.96 / Num. unique obs: 2692 / CC1/2: 0.771 / Rrim(I) all: 1.467

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.07 Å / SU ML: 0.4256 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3668
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 1413 5 %
Rwork0.2218 26854 -
obs0.2236 28267 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5487 82 0 30 5599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00525693
X-RAY DIFFRACTIONf_angle_d0.75767720
X-RAY DIFFRACTIONf_chiral_restr0.0475869
X-RAY DIFFRACTIONf_plane_restr0.0061975
X-RAY DIFFRACTIONf_dihedral_angle_d18.30222141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.36811330.35882557X-RAY DIFFRACTION96.35
2.49-2.590.35211430.31482708X-RAY DIFFRACTION100
2.59-2.70.38581400.2952658X-RAY DIFFRACTION99.89
2.7-2.850.35431420.28282698X-RAY DIFFRACTION99.96
2.85-3.020.31011430.2852718X-RAY DIFFRACTION100
3.02-3.260.34041410.27162694X-RAY DIFFRACTION99.93
3.26-3.580.25861430.23722712X-RAY DIFFRACTION99.86
3.59-4.10.26111360.22932575X-RAY DIFFRACTION94.76
4.1-5.170.22591430.17692719X-RAY DIFFRACTION99.72
5.17-48.070.19911490.18272815X-RAY DIFFRACTION99.6

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