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- PDB-8jr8: MapSPARTA dimer bound with guide-target -

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Basic information

Entry
Database: PDB / ID: 8jr8
TitleMapSPARTA dimer bound with guide-target
Components
  • DNA (25-MER)
  • Piwi domain-containing protein
  • RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
  • TIR domain-containing protein
KeywordsDNA BINDING PROTEIN/DNA/RNA / SPARTA / Ago / Tir / DNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


nucleic acid binding / signal transduction
Similarity search - Function
TIR domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Piwi domain-containing protein / TIR domain-containing protein
Similarity search - Component
Biological speciesMaribacter polysiphoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsHuang, P.P. / Li, Z.X. / Guo, L.J. / Xiao, Y.B. / Chen, M.R.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)Nos.2018YFA0902000 China
Ministry of Science and Technology (MoST, China)ZX-2021ZD0203404 China
National Natural Science Foundation of China (NSFC)Nos. 32271330 China
National Natural Science Foundation of China (NSFC)Nos. 32000889 China
National Natural Science Foundation of China (NSFC)Nos. 31970547 China
CitationJournal: To Be Published
Title: Cryo-EM Structure of MapSPARTA
Authors: Huang, P.P. / Guo, L.J. / Li, Z.X. / Yan, P.R. / Chen, M.R. / Xiao, Y.B.
History
DepositionJun 16, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
F: DNA (25-MER)
G: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')
H: DNA (25-MER)
A: Piwi domain-containing protein
C: Piwi domain-containing protein
D: TIR domain-containing protein
B: TIR domain-containing protein


Theoretical massNumber of molelcules
Total (without water)251,3788
Polymers251,3788
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')


Mass: 6651.949 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: guide RNA / Source: (synth.) Maribacter polysiphoniae (bacteria)
#2: DNA chain DNA (25-MER)


Mass: 7675.000 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: target DNA / Source: (synth.) Maribacter polysiphoniae (bacteria)
#3: Protein Piwi domain-containing protein


Mass: 58091.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Gene: LX92_01809 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A316E3U6
#4: Protein TIR domain-containing protein


Mass: 53270.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Gene: LX92_01810 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A316E683

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Maribacter polysiphoniae short Ago complexed with TIR-APAZ
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79726 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313617
ELECTRON MICROSCOPYf_angle_d0.62618712
ELECTRON MICROSCOPYf_dihedral_angle_d18.6292298
ELECTRON MICROSCOPYf_chiral_restr0.0432008
ELECTRON MICROSCOPYf_plane_restr0.0042105

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