8J7S | pdb_00008j7s

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 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.
HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China. [e-mail].
Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. [e-mail].
New Cornerstone Science Laboratory, Shenzhen, Guangdong, China. [e-mail].

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 
• Modeled 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