The Human LINE-1 ORF2p target-primed reverse transcription complex

2025-05-07 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _em_admin.last_update PDBe PDBe 2024-11-12 2025-03-12 2025-03-12 2025-05-07 UK Research and Innovation (UKRI) MC_UP_1201/19 United Kingdom Jane Coffin Childs (JCC) Fund United States European Molecular Biology Organization (EMBO) European Union The Human LINE-1 ORF2p target-primed reverse transcription complex Ghanim GE Hu H Nguyen THD LINE-1, L1, ORF2p, Reverse transcriptase, endonuclease, DNA, RNA, RNA BINDING PROTEIN Ghanim GE Hu H Boulanger J Nguyen THD Structural mechanism of LINE-1 target-primed reverse transcription. Science US 388 eads8412 eads8412 2025 40048554 doi:10.1126/science.ads8412 1095-9203 0038 SCIEAS EMD-52071 other EM volume

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

EMD-52072 other EM volume

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

EMD-52073 other EM volume

Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved

9hdo FULLOVERLAP Human LINE-1 ORF2p target-primed reverse transcription complex Human LINE-1 ORF2p target-primed reverse transcription complex 0 1 2 3 4 5 6 7

The human LINE-1 retrotransposon mobilizes using the encoded ORF2p protein by a mechanism called target-primed reverse transcription.

Homo sapiens 0.052 ORF2p 1 1

LINE-1 ORF2p protein

Homo sapiens Target DNA 1 2 3 5 6

Target DNA idealized from a de novo LINE-1 insertion into the FVIII gene

Homo sapiens LINE-1 retrotransposable element ORF2 protein Homo sapiens 0.206717625 1 Trichoplusia ni LEVO MVHHHHHHHHGGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTV EHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIY NKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVD LIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAK EFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTV DEALKDAQTNSSSNNNNNNNNNNLGSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQ GKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGGMTGSTSHITILTLNINGLNSAIKRHRLASWIKSQDPSV CCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPN TGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPH HTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELRIKNLTQSRSTTWKLNNLLLNDYWVHNEMKAEIKMFFETNE NKDTTYQNLWDAFKAVCRGKFIALNAYKRKQERSKIDTLTSQLKELEKQEQTHSKASRRQEITKIRAELKEIETQKTLQK INESRSWFFERINKIDRPLARLIKKKREKNQIDTIKNDKGDITTDPTEIQTTIREYYKHLYANKLENLEEMDTFLDTYTL PRLNQEEVESLNRPITGSEIVAIINSLPTKKSPGPDGFTAEFYQRYKEELVPFLLKLFQSIEKEGILPNSFYEASIILIP KPGRDTTKKENFRPISLMNIDAKILNKILANRIQQHIKKLIHHDQVGFIPGMQGWFNIRKSINVIQHINRAKDKNHMIIS IDAEKAFDKIQQPFMLKTLNKLGIDGTYFKIIRAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFNIVLEVLARA IRQEKEIKGIQLGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFLYTNNRQTESQIMGELP FTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEETNKWKNIPCSWVGRINIVKMAILPKVIYRFNAIPIKLPMTFFT ELEKTTLKFIWNQKRARIAKSILSQKNKAGGITLPDFKLYYKATVTKTAWYWYQNRDIDQWNRTEPSEIMPHIYNYLIFD KPEKNKQWGKDSLFNKWCWENWLAICRKLKLDPFLTPYTKINSRWIKDLNVKPKTIKTLEENLGITIQDIGVGKDFMSKT PKAMATKDKIDKWDLIKLKSFCTAKETTIRVNRQPTTWEKIFATYSSDKGLISRIYNELKQIYKKKTNNPIKKWAKDMNR HFSKEDIYAAKKHMKKCSSSLAIREMQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWDCKLVQPLWKSVW RFLRDLELEIPFDPAIPLLGIYPNEYKSCCYKDTCTRMFIAALFTIAKTWNQPKCPTMIDWIKKMWHIYTMEYYAAIKND EFISFVGTWMKLETIILSKLSQEQKTKHRIFSLIGGN P0AEX9 Q12306 O00370 2.7.7.49 Target DNA strand 1 Homo sapiens 0.011424341

Modified from de novo LINE-1 insertion event into the FVIII gene

1 (DT)(DT)(DA)(DG)(DT)(DT)(DG)(DC)(DT)(DG)(DA)(DA)(DT)(DT)(DA)(DT)(DT)(DG)(DG)(DA) (DA)(DG)(DT)(DT)(DT)(DT)(DG)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) DNA Target DNA strand 2 Homo sapiens 0.009144986999999999

Modified from de novo LINE-1 insertion event into the FVIII gene

1 (DA)(DA)(DA)(DC)(DA)(DA)(DA)(DA)(DC)(DT)(DT)(DC)(DC)(DA)(DA)(DT)(DA)(DA)(DT)(DT) (DC)(DA)(DG)(DC)(DA)(DA)(DC)(DT)(DA)(DA) DNA Template P(A)30 RNA Homo sapiens 0.009831217

Chemically synthesized 30 nucleotide Poly(A) sequence

1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA Target DNA strand 3 Homo sapiens 0.007900111999999999

Modified from de novo LINE-1 insertion event into the FVIII gene

1 (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DA)(DT)(DA)(DA)(DA) DNA Target DNA strand 4 Homo sapiens 0.005905972999999999

Modified from de novo LINE-1 insertion event into the FVIII gene

1 (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) DNA Unassigned Nucleic Acid Homo sapiens 0.0012078699999999998 1 (DA)(DA)(DA)(DA) DNA MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 1 ZN 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE 0.00046616899999999995 1 D3T singleParticle particle 8.0 25.0 C8H18N2O4S HEPES 500.0 CH3CO2K potassium acetate 1.5 Mg(CH3COO)2 magnesium acetate 10.0 Zn(CH3COO)2 zinc acetate 1.0 C4H10O2S2 DTT 0.5 C7H7FO2S PMSF Quantifoil R1.2/1.3 GOLD 300 GRAPHENE OXIDE CONTINUOUS GLOW DISCHARGE 2 AIR ETHANE 100 277 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 8.0 22.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 TFS FALCON 4i (4k x 4k) 5.82 60.0 1

All images were processed using RELION5.0 and CryoSPARC 4.5.3

4568277 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab initio

5 C1 2.3 FSC 0.143 CUT-OFF RELION 5 680273 MAXIMUM LIKELIHOOD RELION 5 MAXIMUM LIKELIHOOD RELION 5 6 RELION 5 emd_52070.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 362.9 362.9 362.9 90.0 90.0 90.0 X Y Z -0.040771734 0.079997905 -0.000040908955 0.0013837582 0.955 0.955 0.955 0.011 AUTHOR ::::EMDATABANK.org::::EMD-52070:::: LINE-1 ORF2p TPRT Complex Consensus Sharpened Map A 1-1275 AlphaFold in silico model

Initial model was an alphaFold 2 prediction and was rebuilt into the density.

emd_52070_msk_1.map emd_52070_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 362.9 362.9 362.9 90.0 90.0 90.0 X Y Z -0.014443267 0.037997514 -0.000036813388 0.00057317346 0.955 0.955 0.955 AUTHOR ::::EMDATABANK.org::::EMD-52070:::: LINE-1 ORF2p TPRT Complex Consensus Map emd_52070_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 362.9 362.9 362.9 90.0 90.0 90.0 X Y Z -0.0168252 0.04078104 -0.000036624733 0.00084006635 0.955 0.955 0.955 AUTHOR ::::EMDATABANK.org::::EMD-52070:::: LINE-1 ORF2p TPRT Complex Consensus half-map 1 emd_52070_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 362.9 362.9 362.9 90.0 90.0 90.0 X Y Z -0.016362207 0.04012394 -0.000037011385 0.000840791 0.955 0.955 0.955 AUTHOR ::::EMDATABANK.org::::EMD-52070:::: LINE-1 ORF2p TPRT Complex Consensus half-map 2