7XLT | pdb_00007xlt

Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids

• PDB DOI: https://doi.org/10.2210/pdb7XLT/pdb
• NAKB: 7XLT
• EM Map EMD-33286: EMDB EMDataResource

• Classification: DNA-RNA HYBRID
• Organism(s): Mus musculus, Arabidopsis
• Expression System: Mus musculus, Arabidopsis
• Mutation(s): No 


• Deposited: 2022-04-22 Released: 2022-05-25 
• Deposition Author(s): Li, Q., Lin, C., Luo, Z., Li, H., Li, X., Sun, Q.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids.

Li, Q., Lin, C., Luo, Z., Li, H., Li, X., Sun, Q.

(2022) J Genet Genomics 49: 677-680

• PubMed: 35550870 
• DOI: https://doi.org/10.1016/j.jgg.2022.04.011
• Primary Citation Related Structures: 
  7XLT

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Organizational Affiliation: 
• Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.
Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.
Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China. Electronic address: [e-mail].
Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 73.31 kDa 
• Atom Count: 4,985 
• Modeled Residue Count: 511 
• Deposited Residue Count: 519 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S9.6 Fab HC	A [auth H]	220	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S9.6 Fab LC	B [auth L]	219	Mus musculus	Mutation(s): 0  Gene Names: Igkc, Igk-C

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA	C [auth A]	40	Arabidopsis

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA	D [auth B]	40	Arabidopsis

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-25 
Deposition Author(s): Li, Q., Lin, C., Luo, Z., Li, H., Li, X., Sun, Q.

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Funding Organization	Location	Grant Number
Other private	China	041301470

Revision History  

• Version 1.0: 2022-05-25
  Type: Initial release
  
• Version 1.1: 2022-07-06
  Changes: Database references, Structure summary
• Version 1.2: 2022-08-03
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Structure summary