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- PDB-8alz: Cryo-EM structure of ASCC3 in complex with ASC1 -

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Basic information

Entry
Database: PDB / ID: 8alz
TitleCryo-EM structure of ASCC3 in complex with ASC1
Components
  • Activating signal cointegrator 1
  • Activating signal cointegrator 1 complex subunit 3
KeywordsDNA BINDING PROTEIN / helicase / zinc finger / activator / DNA binding
Function / homology
Function and homology information


ALKBH3 mediated reversal of alkylation damage / RQC-trigger complex / regulation of myoblast differentiation / DNA alkylation repair / ribosome disassembly / DNA repair complex / ribosome-associated ubiquitin-dependent protein catabolic process / DNA 3'-5' helicase / 3'-5' DNA helicase activity / histone acetyltransferase binding ...ALKBH3 mediated reversal of alkylation damage / RQC-trigger complex / regulation of myoblast differentiation / DNA alkylation repair / ribosome disassembly / DNA repair complex / ribosome-associated ubiquitin-dependent protein catabolic process / DNA 3'-5' helicase / 3'-5' DNA helicase activity / histone acetyltransferase binding / ubiquitin-like protein ligase binding / estrogen receptor signaling pathway / cytosolic ribosome / rescue of stalled ribosome / nuclear estrogen receptor binding / nuclear receptor binding / neuromuscular junction / protease binding / transcription coactivator activity / nuclear speck / nuclear body / centrosome / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / protein-containing complex / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / : / TRIP4, third domain / TRI4 N-terminal domain / Sec63 N-terminal domain-like domain / Zinc finger, C2HC5-type / Activating signal cointegrator 1-like / Putative zinc finger motif, C2HC5-type / ASCH / ASCH domain ...: / : / TRIP4, third domain / TRI4 N-terminal domain / Sec63 N-terminal domain-like domain / Zinc finger, C2HC5-type / Activating signal cointegrator 1-like / Putative zinc finger motif, C2HC5-type / ASCH / ASCH domain / ASCH domain / Sec63 N-terminal domain-like fold / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Sec63 domain / Sec63 Brl domain / C2 domain / PUA-like superfamily / C2 domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Arc Repressor Mutant, subunit A / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Activating signal cointegrator 1 / Activating signal cointegrator 1 complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJia, J. / Hilal, T. / Loll, B. / Wahl, M.C.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 130/1064-1 FUGG Germany
German Research Foundation (DFG)GRK 2473 Germany
German Research Foundation (DFG)501_BIS-CryoFac Germany
German Research Foundation (DFG)BO3442/1-2 Germany
German Research Foundation (DFG)SFB860 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of ASCC3 in complex with ASC1
Authors: Jia, J. / Hilal, T. / Loll, B. / Wahl, M.C.
History
DepositionAug 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.2Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activating signal cointegrator 1
B: Activating signal cointegrator 1 complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,0584
Polymers272,9272
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7850 Å2
ΔGint-22 kcal/mol
Surface area87040 Å2
MethodPISA

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Components

#1: Protein Activating signal cointegrator 1 / ASC-1 / Thyroid receptor-interacting protein 4 / TR-interacting protein 4 / TRIP-4


Mass: 66650.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIP4, RQT4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15650
#2: Protein Activating signal cointegrator 1 complex subunit 3 / ASC-1 complex subunit p200 / ASC1p200 / Helicase / ATP binding 1 / Trip4 complex subunit p200


Mass: 206276.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASCC3, HELIC1, RQT2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N3C0, DNA helicase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: ASCC3-ASC1 / Type: COMPLEX
Details: Protein complex was produced in baculovirus-insect system.
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.27 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
Details: Solutions were made fresh from concentrated to avoid microbial contamination.
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMsodium chlorideNaCl1
220 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES-NaOH1
31 mMDithiothreitolDTT1
40.1 mg/mln-dodecyl-B-maltosideDDM1
SpecimenConc.: 4.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 40.57 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6267

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
EM software
IDNameVersionCategory
2EPU2.8image acquisition
4cryoSPARC3.1CTF correction
8PHENIXmodel refinement
10cryoSPARC3.1initial Euler assignment
11cryoSPARC3.1final Euler assignment
13cryoSPARC3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 244064 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316796
ELECTRON MICROSCOPYf_angle_d0.69422764
ELECTRON MICROSCOPYf_dihedral_angle_d4.3112213
ELECTRON MICROSCOPYf_chiral_restr0.0442534
ELECTRON MICROSCOPYf_plane_restr0.0052915

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