Human UPF1 in complex with the histone stem loop RNA

2026-01-21 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 DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2025-04-14 2025-12-03 2025-12-03 2026-01-21 German Research Foundation (DFG) CH1245/5-1, CH1245/6-1 Germany German Research Foundation (DFG) INST 335/589-1 Germany German Research Foundation (DFG) INST 335/590-1 Germany German Research Foundation (DFG) INST 335/590-1 Germany German Research Foundation (DFG) (INST 130/1014-1 Germany EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND 664726 Germany Human UPF1 in complex with the histone stem loop RNA Machado de Amorim A Loll B Hilal T Chakrabarti S ATP-DEPENDENT HELICASE RENT1, UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG, HUPF1, UP FRAMESHIFT, histone stem loop mRNA, HYDROLASE Machado de Amorim A Xue G He W Dittmers T Lewandowski S Perez-Borrajero C Bethmann J Mateva N Krage C Nandana V Loll B Hilal T Hennig J Urlaub H Marzluff WF Chakrabarti S Mechanistic insights into recruitment and regulation of the RNA helicase UPF1 in replication-dependent histone mRNA decay. Nat Commun UK 17 155 155 2026 41484129 doi:10.1038/s41467-025-67991-z 2041-1723 9qwn FULLOVERLAP PDB 2XZL unspecified PDB 4HXH unspecified EMDB EMD-53417 associated EM volume

Upf1 Upf1 0 1 2 Homo sapiens 0.10 Isoform 2 of Regulator of nonsense transcripts 1 Homo sapiens 0.089972188 1 Escherichia coli DH5[alpha] LEVO TKDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLL GFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPS ATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDM RLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVETVHNFQVDFVWKSTSFDRMQSALKTFAVDE TSVSGYIYHKLLGHEVEDVITKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN GPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKR YRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKK AAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQ EEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREK DFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQFS Q92900 3.6.4.12 RNA stem loop synthetic construct 0.011896941999999999 1 UUUUUUUUUUUUCCAAAGGCUCUUUUCAGAGCCACCCA ZINC ION 6.5409e-05 3 ZN singleParticle particle 5.6 7.5 Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY GLOW DISCHARGE ETHANE 100 283 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 2.0 96000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) COUNTING 2 5498 40.57 44.0 1 3102505 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 C1 BACK PROJECTION 3.6 FSC 0.143 CUT-OFF 300222 RANDOM ASSIGNMENT MAXIMUM LIKELIHOOD 3 emd_53417.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 235.87201 235.87201 235.87201 90.0 90.0 90.0 X Y Z -0.0 1.3158137 0.0043509635 0.043056186 0.819 0.819 0.819 0.2 AUTHOR ::::EMDATABANK.org::::EMD-53417:::: emd_53417_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 235.87201 235.87201 235.87201 90.0 90.0 90.0 X Y Z -0.0 1.1504842 0.004254399 0.040579934 0.819 0.819 0.819 AUTHOR ::::EMDATABANK.org::::EMD-53417:::: Map with improved SL density after local classification emd_53417_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 235.87201 235.87201 235.87201 90.0 90.0 90.0 X Y Z -0.32968006 1.4242712 0.0022022056 0.048711702 0.819 0.819 0.819 AUTHOR ::::EMDATABANK.org::::EMD-53417:::: emd_53417_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 235.87201 235.87201 235.87201 90.0 90.0 90.0 X Y Z -0.31565192 1.4452478 0.002192976 0.04900717 0.819 0.819 0.819 AUTHOR ::::EMDATABANK.org::::EMD-53417::::