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- EMDB-53417: Human UPF1 in complex with the histone stem loop RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-53417
TitleHuman UPF1 in complex with the histone stem loop RNA
Map data
Sample
  • Complex: Upf1
    • Protein or peptide: Isoform 2 of Regulator of nonsense transcripts 1
    • RNA: RNA stem loop
  • Ligand: ZINC ION
KeywordsATP-DEPENDENT HELICASE RENT1 / UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG / HUPF1 / UP FRAMESHIFT / histone stem loop mRNA / HYDROLASE
Function / homology
Function and homology information


positive regulation of mRNA cis splicing, via spliceosome / supraspliceosomal complex / double-stranded DNA helicase activity / exon-exon junction complex / cell cycle phase transition / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization ...positive regulation of mRNA cis splicing, via spliceosome / supraspliceosomal complex / double-stranded DNA helicase activity / exon-exon junction complex / cell cycle phase transition / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of telomere maintenance / telomeric DNA binding / nuclear-transcribed mRNA catabolic process / cellular response to interleukin-1 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / P-body / helicase activity / cellular response to lipopolysaccharide / DNA helicase / DNA replication / chromosome, telomeric region / RNA helicase activity / RNA helicase / DNA repair / chromatin binding / chromatin / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, Cys/His rich zinc-binding domain / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / Helicase/UvrB, N-terminal ...RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, Cys/His rich zinc-binding domain / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Regulator of nonsense transcripts 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMachado de Amorim A / Loll B / Hilal T / Chakrabarti S
Funding support Germany, 6 items
OrganizationGrant numberCountry
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 COFUND664726 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Mechanistic insights into recruitment and regulation of the RNA helicase UPF1 in replication-dependent histone mRNA decay.
Authors: Alexandrina Machado de Amorim / Guangpu Xue / Wenxia He / Theresa Dittmers / Sarah Lewandowski / Cecilia Perez-Borrajero / Juliane Bethmann / Nevena Mateva / Clemens Krage / Vidhyadhar ...Authors: Alexandrina Machado de Amorim / Guangpu Xue / Wenxia He / Theresa Dittmers / Sarah Lewandowski / Cecilia Perez-Borrajero / Juliane Bethmann / Nevena Mateva / Clemens Krage / Vidhyadhar Nandana / Bernhard Loll / Tarek Hilal / Janosch Hennig / Henning Urlaub / William F Marzluff / Sutapa Chakrabarti /
Abstract: Metazoan histone mRNAs are a unique class of mRNAs that lack the poly(A) tail present in all other eukaryotic transcripts. Instead, they end in a conserved stem-loop (SL) structure, necessitating a ...Metazoan histone mRNAs are a unique class of mRNAs that lack the poly(A) tail present in all other eukaryotic transcripts. Instead, they end in a conserved stem-loop (SL) structure, necessitating a decay mechanism that is distinct from deadenylation-initiated degradation. Here, combining structural and functional approaches, we elucidate molecular mechanisms of initiation of histone mRNA decay. At the end of S-phase, the RNA helicase UPF1, the exoribonuclease 3'hExo and stem-loop binding protein SLBP all contribute to histone mRNA degradation, although how they are mechanistically coupled remained unknown. The cryoEM structure of an UPF1:SL RNA complex, presented here, shows that binding of UPF1 partially melts the RNA stem in the absence of ATP, harnessing the free energy derived from RNA-binding to unwind RNA. This melting event primes the SL-RNA for decay by 3'hExo. Using biochemical and cellular analyses, we demonstrate that SLBP directly engages the UPF1 helicase core to attenuate its unwinding activity and prevent premature degradation. Activation of UPF1 at a later stage promotes SL-RNA decay. We provide direct evidence that UPF1, SLBP and 3'hExo form a degradosome-like assembly that functionally couples SL unwinding and degradation, highlighting a dynamic and intricate network of UPF1-centric interactions that orchestrates timely histone mRNA decay.
History
DepositionApr 14, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53417.png

Downloads & links

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Map

FileDownload / File: emd_53417.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 288 pix.
= 235.872 Å		0.82 Å/pix.
x 288 pix.
= 235.872 Å		0.82 Å/pix.
x 288 pix.
= 235.872 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.819 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.0 - 1.3158137
Average (Standard dev.)0.0043509635 (±0.043056186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 235.87201 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map with improved SL density after local classification

Fileemd_53417_additional_1.map
AnnotationMap with improved SL density after local classification
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_53417_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53417_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Upf1

EntireName: Upf1
Components
  • Complex: Upf1
    • Protein or peptide: Isoform 2 of Regulator of nonsense transcripts 1
    • RNA: RNA stem loop
  • Ligand: ZINC ION

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Supramolecule #1: Upf1

SupramoleculeName: Upf1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Isoform 2 of Regulator of nonsense transcripts 1

MacromoleculeName: Isoform 2 of Regulator of nonsense transcripts 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.972188 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
SequenceString: TKDLPIHACS YCGIHDPACV VYCNTSKKWF CNGRGNTSGS HIVNHLVRAK CKEVTLHKDG PLGETVLECY NCGCRNVFLL GFIPAKADS VVVLLCRQPC ASQSSLKDIN WDSSQWQPLI QDRCFLSWLV KIPSEQEQLR ARQITAQQIN KLEELWKENP S ATLEDLEK ...String:
TKDLPIHACS YCGIHDPACV VYCNTSKKWF CNGRGNTSGS HIVNHLVRAK CKEVTLHKDG PLGETVLECY NCGCRNVFLL GFIPAKADS VVVLLCRQPC ASQSSLKDIN WDSSQWQPLI QDRCFLSWLV KIPSEQEQLR ARQITAQQIN KLEELWKENP S ATLEDLEK PGVDEEPQHV LLRYEDAYQY QNIFGPLVKL EADYDKKLKE SQTQDNITVR WDLGLNKKRI AYFTLPKTDS DM RLMQGDE ICLRYKGDLA PLWKGIGHVI KVPDNYGDEI AIELRSSVGA PVETVHNFQV DFVWKSTSFD RMQSALKTFA VDE TSVSGY IYHKLLGHEV EDVITKCQLP KRFTAQGLPD LNHSQVYAVK TVLQRPLSLI QGPPGTGKTV TSATIVYHLA RQGN GPVLV CAPSNIAVDQ LTEKIHQTGL KVVRLCAKSR EAIDSPVSFL ALHNQIRNMD SMPELQKLQQ LKDETGELSS ADEKR YRAL KRTAERELLM NADVICCTCV GAGDPRLAKM QFRSILIDES TQATEPECMV PVVLGAKQLI LVGDHCQLGP VVMCKK AAK AGLSQSLFER LVVLGIRPIR LQVQYRMHPA LSAFPSNIFY EGSLQNGVTA ADRVKKGFDF QWPQPDKPMF FYVTQGQ EE IASSGTSYLN RTEAANVEKI TTKLLKAGAK PDQIGIITPY EGQRSYLVQY MQFSGSLHTK LYQEVEIASV DAFQGREK D FIILSCVRAN EHQGIGFLND PRRLNVALTR ARYGVIIVGN PKALSKQPLW NHLLNYYKEQ KVLVEGPLNN LRESLMQFS

UniProtKB: Regulator of nonsense transcripts 1

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Macromolecule #2: RNA stem loop

MacromoleculeName: RNA stem loop / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.896942 KDa
SequenceString:
UUUUUUUUUU UUCCAAAGGC UCUUUUCAGA GCCACCCA

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration5.6 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 5498 / Average exposure time: 40.57 sec. / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3102505
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 300222
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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