9HDQ | pdb_00009hdq

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

PDB DOI: https://doi.org/10.2210/pdb9HDQ/pdb
EM Map EMD-52072: EMDB EMDataResource
NAKB: 9HDQ

Classification: RNA BINDING PROTEIN
Organism(s): Escherichia coli K-12, Saccharomyces cerevisiae S288C, Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-11-12 Released: 2025-03-12
Deposition Author(s): Ghanim, G.E., Hu, H., Nguyen, T.H.D.
Funding Organization(s): UK Research and Innovation (UKRI), Jane Coffin Childs (JCC) Fund, European Molecular Biology Organization (EMBO)

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

PubMed: 40048554 Search on PubMed
DOI: https://doi.org/10.1126/science.ads8412
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 252.2 kDa
Atom Count: 10,261
Modeled Residue Count: 1,110
Deposited Residue Count: 1,943
Unique protein chains: 1
Unique nucleic acid chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LINE-1 retrotransposable element ORF2 protein	A	1,797	Escherichia coli K-12, Saccharomyces cerevisiae S288C, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: malE, b4034, JW3994, SMT3, YDR510W, D9719.15 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00370
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
Target DNA strand 1	B	37	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
Target DNA strand 2	C	30	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
Template P(A)30 RNA	D	30	Homo sapiens
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Molecule	Chains	Length	Organism
Entity ID: 5
Target DNA strand 3	E	26	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
Target DNA strand 4	F	19	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
Unassigned Nucleic Acid	G	4	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1-5286
MODEL REFINEMENT	Servalcat	0.4.72
RECONSTRUCTION	RELION	5

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Ghanim, G.E.

Hu, H.

Nguyen, T.H.D.

Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	MC_UP_1201/19
Jane Coffin Childs (JCC) Fund	United States	--
European Molecular Biology Organization (EMBO)	European Union	--