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- EMDB-62127: Structure of human LINE-1 ORF2p with endogenous DNA and RNA/cDNA ... -

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Basic information

Entry
Database: EMDB / ID: EMD-62127
TitleStructure of human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound to dNTP and Mn2+
Map data
Sample
  • Complex: Human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound to dNTP and Mn2+
    • Complex: Human LINE-1 ORF2p
      • Protein or peptide: LINE-1 retrotransposable element ORF2 protein
    • Complex: endogenous DNA and RNA/cDNA hybrid
      • DNA: Genomic DNA (top strand)
      • DNA: Genomic DNA (bottom strand)
      • DNA: Complementary DNA
      • RNA: Template RNA
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION
KeywordsEndonuclease / Reverse transcriptase / GENE REGULATION
Function / homology
Function and homology information


nucleic acid metabolic process / retrotransposition / type II site-specific deoxyribonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / DNA recombination / RNA binding / metal ion binding
Similarity search - Function
Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
LINE-1 retrotransposable element ORF2 protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Trichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsJin W / Yu C / Xu RM
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32330021 China
National Natural Science Foundation of China (NSFC)92153302 China
Chinese Academy of SciencesXDB3701010 China
CitationJournal: Science / Year: 2025
Title: Mechanism of DNA targeting by human LINE-1.
Authors: Wenxing Jin / Cong Yu / Yan Zhang / Changchang Cao / Tianfan Xia / Ge Song / Zhaokui Cai / Yuanchao Xue / Bing Zhu / Rui-Ming Xu /
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 ...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.
History
DepositionOct 22, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62127.png

Downloads & links

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Map

FileDownload / File: emd_62127.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 384 pix.
= 384. Å		1 Å/pix.
x 384 pix.
= 384. Å		1 Å/pix.
x 384 pix.
= 384. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-2.3638625 - 2.978786
Average (Standard dev.)0.00006814531 (±0.041592512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62127_msk_1.map
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Additional map: #1

Fileemd_62127_additional_1.map
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Half map: #2

Fileemd_62127_half_map_1.map
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Half map: #1

Fileemd_62127_half_map_2.map
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Sample components

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Entire : Human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound ...

EntireName: Human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound to dNTP and Mn2+
Components
  • Complex: Human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound to dNTP and Mn2+
    • Complex: Human LINE-1 ORF2p
      • Protein or peptide: LINE-1 retrotransposable element ORF2 protein
    • Complex: endogenous DNA and RNA/cDNA hybrid
      • DNA: Genomic DNA (top strand)
      • DNA: Genomic DNA (bottom strand)
      • DNA: Complementary DNA
      • RNA: Template RNA
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound ...

SupramoleculeName: Human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound to dNTP and Mn2+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4, #3, #5

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Supramolecule #2: Human LINE-1 ORF2p

SupramoleculeName: Human LINE-1 ORF2p / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: endogenous DNA and RNA/cDNA hybrid

SupramoleculeName: endogenous DNA and RNA/cDNA hybrid / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Source (natural)Organism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: LINE-1 retrotransposable element ORF2 protein

MacromoleculeName: LINE-1 retrotransposable element ORF2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 149.153141 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: TGSTSHITIL TLNINGLNSA IKRHRLASWI KSQDPSVCCI QETHLTCRDT HRLKIKGWRK IYQANGKQKK AGVAILVSDK TDFKPTKIK RDKEGHYIMV KGSIQQEELT ILNIYAPNTG APRFIKQVLS DLQRDLDSHT LIMGDFNTPL STLDRSTRQK V NKDTQELN ...String:
TGSTSHITIL TLNINGLNSA IKRHRLASWI KSQDPSVCCI QETHLTCRDT HRLKIKGWRK IYQANGKQKK AGVAILVSDK TDFKPTKIK RDKEGHYIMV KGSIQQEELT ILNIYAPNTG APRFIKQVLS DLQRDLDSHT LIMGDFNTPL STLDRSTRQK V NKDTQELN SALHQADLID IYRTLHPKST EYTFFSAPHH TYSKIDHIVG SKALLSKCKR TEIITNYLSD HSAIKLELRI KN LTQSRST TWKLNNLLLN DYWVHNEMKA EIKMFFETNE NKDTTYQNLW DAFKAVCRGK FIALNAYKRK QERSKIDTLT SQL KELEKQ EQTHSKASRR QEITKIRAEL KEIETQKTLQ KINESRSWFF ERINKIDRPL ARLIKKKREK NQIDTIKNDK GDIT TDPTE IQTTIREYYK HLYANKLENL EEMDTFLDTY TLPRLNQEEV ESLNRPITGS EIVAIINSLP TKKSPGPDGF TAEFY QRYK EELVPFLLKL FQSIEKEGIL PNSFYEASII LIPKPGRDTT KKENFRPISL MNIDAKILNK ILANRIQQHI KKLIHH DQV GFIPGMQGWF NIRKSINVIQ HINRAKDKNH MIISIDAEKA FDKIQQPFML KTLNKLGIDG TYFKIIRAIY DKPTANI IL NGQKLEAFPL KTGTRQGCPL SPLLFNIVLE VLARAIRQEK EIKGIQLGKE EVKLSLFADD MIVYLENPIV SAQNLLKL I SNFSKVSGYK INVQKSQAFL YTNNRQTESQ IMGELPFTIA SKRIKYLGIQ LTRDVKDLFK ENYKPLLKEI KEETNKWKN IPCSWVGRIN IVKMAILPKV IYRFNAIPIK LPMTFFTELE KTTLKFIWNQ KRARIAKSIL SQKNKAGGIT LPDFKLYYKA TVTKTAWYW YQNRDIDQWN RTEPSEIMPH IYNYLIFDKP EKNKQWGKDS LFNKWCWENW LAICRKLKLD PFLTPYTKIN S RWIKDLNV KPKTIKTLEE NLGITIQDIG VGKDFMSKTP KAMATKDKID KWDLIKLKSF CTAKETTIRV NRQPTTWEKI FA TYSSDKG LISRIYNELK QIYKKKTNNP IKKWAKDMNR HFSKEDIYAA KKHMKKCSSS LAIREMQIKT TMRYHLTPVR MAI IKKSGN NRCWRGCGEI GTLLHCWWDC KLVQPLWKSV WRFLRDLELE IPFDPAIPLL GIYPNEYKSC CYKDTCTRMF IAAL FTIAK TWNQPKCPTM IDWIKKMWHI YTMEYYAAIK NDEFISFVGT WMKLETIILS KLSQEQKTKH RIFSLIGGN

UniProtKB: LINE-1 retrotransposable element ORF2 protein

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Macromolecule #2: Genomic DNA (top strand)

MacromoleculeName: Genomic DNA (top strand) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 6.026977 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)

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Macromolecule #3: Genomic DNA (bottom strand)

MacromoleculeName: Genomic DNA (bottom strand) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 3.605356 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)

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Macromolecule #4: Complementary DNA

MacromoleculeName: Complementary DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 3.08711 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)

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Macromolecule #5: Template RNA

MacromoleculeName: Template RNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 3.629032 KDa
SequenceString:
UUUUUUUUUU UU

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Macromolecule #6: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DTP
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Details: 20 mM HEPES pH 7.0, 500 mM NaCl, 1 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 268644
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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