9K6I | pdb_00009k6i

Structure of full-length human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1126/science.adu3433
  • Primary Citation of 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.

    • Organizational Affiliation: 
    • State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LINE-1 retrotransposable element ORF2 protein1,274Homo sapiensMutation(s): 15 
EC: 2.7.7.49 (PDB Primary Data), 3.1.21 (PDB Primary Data)
UniProt
Find proteins for O00370 (Homo sapiens)
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Go to UniProtKB:  O00370
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00370
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Genomic DNA (top strand)20Trichoplusia ni
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Entity ID: 3
MoleculeChains LengthOrganismImage
Genomic DNA (bottom strand)12Trichoplusia ni
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Entity ID: 4
MoleculeChains LengthOrganismImage
Complementary DNA10Trichoplusia ni
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Entity ID: 5
MoleculeChains LengthOrganismImage
Template RNAE [auth F]12Trichoplusia ni
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32330021
National Natural Science Foundation of China (NSFC)China92153302
Chinese Academy of SciencesChinaXDB3701010

Revision History  (Full details and data files)

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