9K6G | pdb_00009k6g

Structure of human LINE-1 ORF2p with endogenous dsDNA and RNA/cDNA hybrid

• PDB DOI: https://doi.org/10.2210/pdb9K6G/pdb
• EM Map EMD-62126: EMDB EMDataResource
• NAKB: 9K6G

• Classification: GENE REGULATION
• Organism(s): Homo sapiens, Trichoplusia ni
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2024-10-22 Released: 2025-10-22 
• Deposition Author(s): Jin, W., Yu, C., Xu, R.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of DNA targeting by human LINE-1.

Jin, W., Yu, C., Zhang, Y., Cao, C., Xia, T., Song, G., Cai, Z., Xue, Y., Zhu, B., Xu, R.M.

(2025) Science 390: eadu3433-eadu3433

• PubMed: 41066570 
• DOI: https://doi.org/10.1126/science.adu3433
• Primary Citation Related Structures: 
  9K6G, 9K6H, 9K6I


• PubMed Abstract: 
  

  Long interspersed nuclear element-1 (LINE-1 or L1), the only autonomously active retrotransposon in humans today, constitutes a large proportion of the genome and continues to evolve the genome and impact fundamental biological processes. L1 retrotransposition critically depends on its endonuclease and reverse transcriptase subunit open reading frame 2 protein (ORF2p), which targets genomic loci and nicks DNA using an evolutionarily distinct yet not fully understood mechanism. Our structural and biochemical analyses revealed that ORF2p is a structure-dependent endonuclease. It binds a double-stranded DNA region upstream of the nicking site and recognizes a downstream forked or flap structure for efficient DNA nicking. This discovery suggests that L1 mobilization piggybacks on chromosomal processes with noncanonical DNA structure intermediates.

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Organizational Affiliation: 
• State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 165.57 kDa 
• Atom Count: 9,620 
• Modeled Residue Count: 1,082 
• Deposited Residue Count: 1,328 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LINE-1 retrotransposable element ORF2 protein	A	1,274	Homo sapiens	Mutation(s): 15  EC: 2.7.7.49 (PDB Primary Data), 3.1.21 (PDB Primary Data)
UniProt
Find proteins for O00370 (Homo sapiens) Explore O00370  Go to UniProtKB:  O00370

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Genomic DNA (top strand)	B	20	Trichoplusia ni

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Complementary DNA	C [auth D]	10	Trichoplusia ni

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Genomic DNA (bottom strand)	D [auth C]	12	Trichoplusia ni

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Template RNA	E [auth F]	12	Trichoplusia ni

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Jin, W., Yu, C., Xu, R.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32330021
National Natural Science Foundation of China (NSFC)	China	92153302
Chinese Academy of Sciences	China	XDB3701010

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release