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Basic information

Entry
Database: EMDB / ID: EMD-71834
TitleCryo-EM structure of the DCAF11 E3 ligase bound to the DDX18 helicase mediated by GSH-M12 (consensus refinement)
Map dataConsensus map for DDX18-GSHM12-DCAF11-DDB1 ternary complex
Sample
  • Complex: Ternary complex of the E3 ligase DCAF11 and the helicase DDX18 mediated by GSH-M12
    • Protein or peptide: DCAF11
    • Protein or peptide: DDX18
    • Protein or peptide: DDB1
Keywordsglutathionylation / degradation / E3 ligase / helicase / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsWachter F / Jin CY / Yoon H / Ebert BL / Fischer ES
Funding support United States, 2 items
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 CY / Yoon H / Ebert BL / Fischer ES
History
DepositionJul 27, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71834.png

Downloads & links

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Map

FileReleased
AnnotationConsensus map for DDX18-GSHM12-DCAF11-DDB1 ternary complex
Voxel sizeX=Y=Z: 0.73 Å
Density
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.09372572 - 0.20498946
Average (Standard dev.)0.0000043202867 (±0.004250082)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71834_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of the E3 ligase DCAF11 and the helicase DDX18 me...

EntireName: Ternary complex of the E3 ligase DCAF11 and the helicase DDX18 mediated by GSH-M12
Components
  • Complex: Ternary complex of the E3 ligase DCAF11 and the helicase DDX18 mediated by GSH-M12
    • Protein or peptide: DCAF11
    • Protein or peptide: DDX18
    • Protein or peptide: DDB1

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Supramolecule #1: Ternary complex of the E3 ligase DCAF11 and the helicase DDX18 me...

SupramoleculeName: Ternary complex of the E3 ligase DCAF11 and the helicase DDX18 mediated by GSH-M12
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DCAF11

MacromoleculeName: DCAF11 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVGLNDIFE AQKIEWHEGG GGSGENLYFQ GGGRMGSRNS SSAGSGSGDP SEGLPRRGAG LRRSEEEEEE DEDVDLAQV LAYLLRRGQV RLVQGGGAAN LQFIQALLDS EEENDRAWDG RLGDRYNPPV DATPDTRELE FNEIKTQVEL A TGQLGLRR ...String:
MDWSHPQFEK SAVGLNDIFE AQKIEWHEGG GGSGENLYFQ GGGRMGSRNS SSAGSGSGDP SEGLPRRGAG LRRSEEEEEE DEDVDLAQV LAYLLRRGQV RLVQGGGAAN LQFIQALLDS EEENDRAWDG RLGDRYNPPV DATPDTRELE FNEIKTQVEL A TGQLGLRR AAQKHSFPRM LHQRERGLCH RGSFSLGEQS RVISHFLPND LGFTDSYSQK AFCGIYSKDG QIFMSACQDQ TI RLYDCRY GRFRKFKSIK ARDVGWSVLD VAFTPDGNHF LYSSWSDYIH ICNIYGEGDT HTALDLRPDE RRFAVFSIAV SSD GREVLG GANDGCLYVF DREQNRRTLQ IESHEDDVNA VAFADISSQI LFSGGDDAIC KVWDRRTMRE DDPKPVGALA GHQD GITFI DSKGDARYLI SNSKDQTIKL WDIRRFSSRE GMEASRQAAT QQNWDYRWQQ VPKKAWRKLK LPGDSSLMTY RGHGV LHTL IRCRFSPIHS TGQQFIYSGC STGKVVVYDL LSGHIVKKLT NHKACVRDVS WHPFEEKIVS SSWDGNLRLW QYRQAE YFQ DDMPESEECA SAPAPVPQSS TPFSSPQ

UniProtKB: DDB1- and CUL4-associated factor 11

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Macromolecule #2: DDX18

MacromoleculeName: DDX18 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDYKDDDDKS AVDENLYFQG GGRTGAFEDT SFASLCNLVN ENTLKAIKEM GFTNMTEIQH KSIRPLLEGR DLLAAAKTGS GKTLAFLIP AVELIVKLRF MPRNGTGVLI LSPTRELAMQ TFGVLKELMT HHVHTYGLIM GGSNRSAEAQ KLGNGINIIV A TPGRLLDH ...String:
MDYKDDDDKS AVDENLYFQG GGRTGAFEDT SFASLCNLVN ENTLKAIKEM GFTNMTEIQH KSIRPLLEGR DLLAAAKTGS GKTLAFLIP AVELIVKLRF MPRNGTGVLI LSPTRELAMQ TFGVLKELMT HHVHTYGLIM GGSNRSAEAQ KLGNGINIIV A TPGRLLDH MQNTPGFMYK NLQCLVIDEA DRILDVGFEE ELKQIIKLLP TRRQTMLFSA TQTRKVEDLA RISLKKEPLY VG VDDDKAN ATVDGLEQGY VVCPSEKRFL LLFTFLKKNR KKKLMVFFSS CMSVKYHYEL LNYIDLPVLA IHGKQKQNKR TTT FFQFCN ADSGTLLCTD VAARGLDIPE VDWIVQYDPP DDPKEYIHRV GRTARGLNGR GHALLILRPE ELGFLRYLKQ SKVP LSEFD FSWSKISDIQ SQLEKLIEKN YFLHKSAQEA YKSYIRAYDS HSLKQIFNVN NLNLPQVALS FGFKVPPFVD LNV

UniProtKB: ATP-dependent RNA helicase DDX18

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Macromolecule #3: DDB1

MacromoleculeName: DDB1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH SAAHIVMVDA YKPTKGGRMS YNYVVTAQKP TAVNGCVTGH FTSAEDLNLL IAKNTRLEIY VVTAEGLRPV KEVGMYGKIA VMELFRPKGE SKDLLFILTA KYNACILEYK QSGESIDIIT RAHGNVQDRI GRPSETGIIG IIDPECRMIG LRLYDGLFKV ...String:
MGSSHHHHHH SAAHIVMVDA YKPTKGGRMS YNYVVTAQKP TAVNGCVTGH FTSAEDLNLL IAKNTRLEIY VVTAEGLRPV KEVGMYGKIA VMELFRPKGE SKDLLFILTA KYNACILEYK QSGESIDIIT RAHGNVQDRI GRPSETGIIG IIDPECRMIG LRLYDGLFKV IPLDRDNKEL KAFNIRLEEL HVIDVKFLYG CQAPTICFVY QDPQGRHVKT YEVSLREKEF NKGPWKQENV EAEASMVIAV PEPFGGAIII GQESITYHNG DKYLAIAPPI IKQSTIVCHN RVDPNGSRYL LGDMEGRLFM LLLEKEEQMD GTVTLKDLRV ELLGETSIAE CLTYLDNGVV FVGSRLGDSQ LVKLNVDSNE QGSYVVAMET FTNLGPIVDM CVVDLERQGQ GQLVTCSGAF KEGSLRIIRN GIGGNGNSGE IQKLHIRTVP LYESPRKICY QEVSQCFGVL SSRIEVQDTS GGTTALRPSA STQALSSSVS SSKLFSSSTA PHETSFGEEV EVHNLLIIDQ HTFEVLHAHQ FLQNEYALSL VSCKLGKDPN TYFIVGTAMV YPEEAEPKQG RIVVFQYSDG KLQTVAEKEV KGAVYSMVEF NGKLLASINS TVRLYEWTTE KELRTECNHY NNIMALYLKT KGDFILVGDL MRSVLLLAYK PMEGNFEEIA RDFNPNWMSA VEILDDDNFL GAENAFNLFV CQKDSAATTD EERQHLQEVG LFHLGEFVNV FCHGSLVMQN LGETSTPTQG SVLFGTVNGM IGLVTSLSES WYNLLLDMQN RLNKVIKSVG KIEHSFWRSF HTERKTEPAT GFIDGDLIES FLDISRPKMQ EVVANLQYDD GSGMKREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

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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

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
5.0 mMC9H15O6PTCEP

Details: 50mM HEPES pH 7.4 200mM NaCl 5 mM TCEP
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 10632 / Average exposure time: 3.16 sec. / Average electron dose: 52.004 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: 0.6 µm / Nominal magnification: 165000
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

DetailsMotion corrected on the fly as implemented in cryosparc live
Particle selectionNumber selected: 3767503 / Details: Topaz
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Details: As implemented in cryosparc live / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Details: As in Cryosparc / Number images used: 136583
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 12 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1-v4

chain_id: A, source_name: AlphaFold, initial_model_type: in silico model

5fqd

chain_id: A, source_name: PDB, initial_model_type: experimental model

1-v4

chain_id: A, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: OTHER / Target criteria: real space correlation

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