9HDQ | pdb_00009hdq

The Human LINE-1 ORF2p target-primed reverse transcription complex with the fingers domain in an open conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural mechanism of LINE-1 target-primed reverse transcription.

Ghanim, G.E.Hu, H.Boulanger, J.Nguyen, T.H.D.

(2025) Science 388: eads8412-eads8412

  • DOI: https://doi.org/10.1126/science.ads8412
  • Primary Citation of Related Structures:  
    9HDO, 9HDP, 9HDQ, 9HDR

  • PubMed Abstract: 

    Long interspersed element-1 (LINE-1) retrotransposons are the only active autonomous transposable elements in humans. They propagate by reverse transcribing their mRNA into new genomic locations by a process called target-primed reverse transcription (TPRT). Here, we present four cryo-electron microscopy structures of the human LINE-1 TPRT complex, revealing the conformational dynamics of ORF2p and its extensive remodeling of the target DNA for TPRT initiation. We observe nicking of the DNA second strand during reverse transcription of the first strand. Structure prediction identifies high-confidence binding sites for LINE-1-associated factors, namely PCNA and PABPC1, on ORF2p. Together with our structural data, this suggests a mechanism by which these factors regulate retrotransposition and proposes a model for TPRT that accounts for retrotransposition outcomes observed in cells.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LINE-1 retrotransposable element ORF2 protein1,797Escherichia coli K-12Saccharomyces cerevisiae S288CHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994SMT3YDR510WD9719.15
EC: 2.7.7.49 (PDB Primary Data), 3.1.21 (PDB Primary Data)
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for O00370 (Homo sapiens)
Explore O00370 
Go to UniProtKB:  O00370
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO00370Q12306P0AEX9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
Target DNA strand 137Homo sapiens
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
Target DNA strand 230Homo sapiens
Sequence Annotations
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Entity ID: 4
MoleculeChains LengthOrganismImage
Template P(A)30 RNA30Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
Target DNA strand 326Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
Target DNA strand 419Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
Unassigned Nucleic Acid4Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1-5286
MODEL REFINEMENTServalcat0.4.72
RECONSTRUCTIONRELION5

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomMC_UP_1201/19
Jane Coffin Childs (JCC) FundUnited States--
European Molecular Biology Organization (EMBO)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-07
    Changes: Data collection, Database references