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- PDB-8j7s: Structure of the SPARTA complex -

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Basic information

Entry
Database: PDB / ID: 8j7s
TitleStructure of the SPARTA complex
Components
  • DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3')
  • 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*A)-3')
  • TIR domain-containing protein
KeywordsIMMUNE SYSTEM/RNA/DNA / complex / immune / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA-DNA 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: 2.84 Å
AuthorsGuo, M. / Zhu, Y. / Lin, Z. / Huang, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31825008, 31422014, U21A20276, China
CitationJournal: Cell Res / Year: 2023
Title: Cryo-EM structure of the ssDNA-activated SPARTA complex.
Authors: Minghui Guo / Yuwei Zhu / Zhiying Lin / Dehui Yang / Anqi Zhang / Changyou Guo / Zhiwei Huang /
History
DepositionApr 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Piwi domain-containing protein
B: TIR domain-containing protein
C: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3')
D: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3')
E: Piwi domain-containing protein
F: TIR domain-containing protein
G: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3')
H: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3')
I: Piwi domain-containing protein
J: TIR domain-containing protein
K: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3')
L: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3')
M: Piwi domain-containing protein
N: TIR domain-containing protein
O: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3')
P: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)483,20516
Polymers483,20516
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Piwi domain-containing protein


Mass: 57978.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Gene: LX92_01809 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A316E3U6
#2: Protein
TIR domain-containing protein


Mass: 49396.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Gene: LX92_01810 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A316E683
#3: RNA chain
RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3')


Mass: 6000.577 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Maribacter polysiphoniae (bacteria)
#4: DNA chain
DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3')


Mass: 7425.842 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Maribacter polysiphoniae (bacteria)

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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: SPARTA complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20_4459: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 832006 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00332936
ELECTRON MICROSCOPYf_angle_d0.64745239
ELECTRON MICROSCOPYf_dihedral_angle_d16.4135515
ELECTRON MICROSCOPYf_chiral_restr0.0424982
ELECTRON MICROSCOPYf_plane_restr0.0045119

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