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- PDB-9qwn: Human UPF1 in complex with the histone stem loop RNA -

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Basic information

Entry
Database: PDB / ID: 9qwn
TitleHuman UPF1 in complex with the histone stem loop RNA
Components
  • Isoform 2 of Regulator of nonsense transcripts 1
  • RNA stem loop
KeywordsHYDROLASE / ATP-DEPENDENT HELICASE RENT1 / UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG / HUPF1 / UP FRAMESHIFT / histone stem loop mRNA
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 / positive regulation of mRNA catabolic process / telomere maintenance via semi-conservative replication / 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 / positive regulation of mRNA catabolic process / telomere maintenance via semi-conservative replication / 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
RNA / RNA (> 10) / Regulator of nonsense transcripts 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMachado de Amorim, A. / Loll, B. / Hilal, T. / Chakrabarti, S.
Funding support Germany, 6items
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: To Be Published
Title: Human UPF1 in complex with the histone stem loop RNA
Authors: Machado de Amorim, A. / Loll, B. / Hilal, T. / Chakrabarti, S.
History
DepositionApr 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Regulator of nonsense transcripts 1
D: RNA stem loop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0655
Polymers101,8692
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Isoform 2 of Regulator of nonsense transcripts 1 / ATP-dependent helicase RENT1 / Nonsense mRNA reducing factor 1 / NORF1 / Up-frameshift suppressor 1 ...ATP-dependent helicase RENT1 / Nonsense mRNA reducing factor 1 / NORF1 / Up-frameshift suppressor 1 homolog / hUpf1


Mass: 89972.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPF1, KIAA0221, RENT1 / Plasmid: pet28a / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q92900, DNA helicase, RNA helicase
#2: RNA chain RNA stem loop


Mass: 11896.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Upf1 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.10 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli DH5[alpha] (bacteria) / Plasmid: vector
Buffer solutionpH: 7.5
SpecimenConc.: 5.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 40.57 sec. / Electron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 5498

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3102505
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300222 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 198.86 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00247009
ELECTRON MICROSCOPYf_angle_d0.5249607
ELECTRON MICROSCOPYf_chiral_restr0.04071100
ELECTRON MICROSCOPYf_plane_restr0.00361154
ELECTRON MICROSCOPYf_dihedral_angle_d13.89491219

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