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- PDB-9ptu: Cryo-EM structure of the DCAF11 E3 ligase bound to the DDX18 heli... -

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Basic information

Entry
Database: PDB / ID: 9ptu
TitleCryo-EM structure of the DCAF11 E3 ligase bound to the DDX18 helicase mediated by GSH-M12
Components
  • ATP-dependent RNA helicase DDX18
  • DDB1- and CUL4-associated factor 11
  • DNA damage-binding protein 1
KeywordsLIGASE / glutathionylation / degradation / E3 ligase / helicase
Function / homology
Function and homology information


regulation of mitotic cytokinesis / regulation of cellular response to stress / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex ...regulation of mitotic cytokinesis / regulation of cellular response to stress / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to estradiol stimulus / nucleotide-excision repair / sperm end piece / regulation of circadian rhythm / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Wnt signaling pathway / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / chromosome / site of double-strand break / sperm principal piece / Neddylation / sperm midpiece / ubiquitin-dependent protein catabolic process / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / chromosome, telomeric region / RNA helicase activity / RNA helicase / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / ATP hydrolysis activity / protein-containing complex / : / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
WD repeat protein DCAF11/LEC14B / : / DDX18/Has1, DEAD-box helicase domain / Domain of unknown function DUF4217 / ATP-dependent rRNA helicase SPB4-like, C-terminal extension / DUF4217 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / : ...WD repeat protein DCAF11/LEC14B / : / DDX18/Has1, DEAD-box helicase domain / Domain of unknown function DUF4217 / ATP-dependent rRNA helicase SPB4-like, C-terminal extension / DUF4217 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / WD domain, G-beta repeat / 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 / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 11 / ATP-dependent RNA helicase DDX18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsWachter, F. / Jin, C.Y. / Yoon, H. / Ebert, B.L. / Fischer, E.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1 K99GM154065-01A1 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA214608-09 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the DCAF11 E3 ligase bound to the DDX18 helicase mediated by GSH-M12
Authors: Wachter, F. / Jin, C.Y. / Yoon, H. / Ebert, B.L. / Fischer, E.S.
History
DepositionJul 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DDB1- and CUL4-associated factor 11
C: ATP-dependent RNA helicase DDX18
B: DNA damage-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,8244
Polymers217,2393
Non-polymers5851
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 DDB1- and CUL4-associated factor 11 / WD repeat-containing protein 23


Mass: 66606.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF11, WDR23, GL014, PRO2389 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8TEB1
#2: Protein ATP-dependent RNA helicase DDX18 / DEAD box protein 18 / Myc-regulated DEAD box protein / MrDb


Mass: 54206.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX18, cPERP-D / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVP1, RNA helicase
#3: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 96425.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531
#4: Chemical ChemComp-A1CK5 / L-gamma-glutamyl-S-{6-chloro-5-[(3,5-dimethylphenoxy)carbonyl]-3-fluoropyridin-2-yl}-L-cysteinylglycine


Mass: 585.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26ClFN4O8S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Ternary complex of the E3 ligase DCAF11 and the helicase DDX18 mediated by GSH-M12
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.4 / Details: 50mM HEPES pH 7.4 200mM NaCl 5 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2200 mMsodium chlorideNaCl1
35 mMTCEPC9H15O6P1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283.15 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: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.16 sec. / Electron dose: 52.004 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10632

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.5aparticle selection
2PHENIX1.21.2_5419+SVNmodel refinement
5cryoSPARC4.5.3CTF correction
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
12cryoSPARC4.5.3classification
13cryoSPARC4.6.23D reconstruction
Image processingDetails: Motion corrected on the fly as implemented in cryosparc live
CTF correctionDetails: As implemented in cryosparc live / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3767503 / Details: Topaz
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136583 / Algorithm: FOURIER SPACE / Details: As in cryosparc / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: real space correlation
Atomic model building

3D fitting-ID: 1 / Chain-ID: A

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDSource nameType
1AF-Q8TEB1-F1-v41AlphaFoldin silico model
25FQD

5fqd

A5FQD2PDBexperimental model
3AF-Q9NVP1-F1-v43AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 73.54 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003511706
ELECTRON MICROSCOPYf_angle_d0.736715815
ELECTRON MICROSCOPYf_chiral_restr0.04821732
ELECTRON MICROSCOPYf_plane_restr0.01042045
ELECTRON MICROSCOPYf_dihedral_angle_d5.52251596

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