8J7S

Structure of the SPARTA complex

• PDB DOI: https://doi.org/10.2210/pdb8J7S/pdb
• NAKB: 8J7S
• EM Map EMD-36047: EMDB EMDataResource

• Classification: IMMUNE SYSTEM/RNA/DNA
• Organism(s): Maribacter polysiphoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-28 Released: 2024-03-06 
• Deposition Author(s): Guo, M., Zhu, Y., Lin, Z., Huang, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.84 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the ssDNA-activated SPARTA complex.

Guo, M., Zhu, Y., Lin, Z., Yang, D., Zhang, A., Guo, C., Huang, Z.

(2023) Cell Res 33: 731-734

• PubMed: 37491603 
• DOI: https://doi.org/10.1038/s41422-023-00850-y
• Primary Citation of Related Structures:  
  8J7S

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Organizational Affiliation: 

HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A4B4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 483.21 kDa 
• Atom Count: 31,812 
• Modelled Residue Count: 3,651 
• Deposited Residue Count: 3,868 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Piwi domain-containing protein	A, E, I, M	506	Maribacter polysiphoniae	Mutation(s): 0  Gene Names: LX92_01809
UniProt
Find proteins for A0A316E3U6 (Maribacter polysiphoniae) Explore A0A316E3U6  Go to UniProtKB:  A0A316E3U6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TIR domain-containing protein	B, F, J, N	418	Maribacter polysiphoniae	Mutation(s): 0  Gene Names: LX92_01810
UniProt
Find proteins for A0A316E683 (Maribacter polysiphoniae) Explore A0A316E683  Go to UniProtKB:  A0A316E683

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3')	C, G, K, O	19	Maribacter polysiphoniae

Entity ID: 4
Molecule	Chains	Length	Organism	Image
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')	D, H, L, P	24	Maribacter polysiphoniae

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.84 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20_4459:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Guo, M., Zhu, Y., Lin, Z., Huang, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31825008, 31422014, U21A20276,

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release