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- EMDB-64553: Structure of the human DCAF2-DDB1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64553
TitleStructure of the human DCAF2-DDB1 complex
Map dataCryo-EM map of the human DCAF2-DDB1 complex
Sample
  • Complex: Structure of the human DCAF2-DDB1 complex
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Denticleless protein homolog
KeywordsE3 ligase / ligase
Function / homology
Function and homology information


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 / mitotic G2 DNA damage checkpoint signaling ...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 / mitotic G2 DNA damage checkpoint signaling / 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 / positive regulation of G2/M transition of mitotic cell cycle / cullin family protein binding / ectopic germ cell programmed cell death / protein monoubiquitination / response to UV / positive regulation of viral genome replication / translesion synthesis / proteasomal protein catabolic process / positive regulation of gluconeogenesis / 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 / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Wnt signaling pathway / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / protein polyubiquitination / 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 / nuclear membrane / ubiquitin-dependent protein catabolic process / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / DNA replication / chromosome, telomeric region / regulation of cell cycle / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / centrosome / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / protein-containing complex / : / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / 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 / WD domain, G-beta repeat / WD40 repeat, conserved site ...: / : / 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 / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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
Similarity search - Domain/homology
DNA damage-binding protein 1 / Denticleless protein homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsShen M / Zhang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100980 China
CitationJournal: To Be Published
Title: Structure of the human DCAF2-DDB1 complex
Authors: Shen M / Zhang H
History
DepositionMay 12, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64553.png

Downloads & links

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Map

FileDownload / File: emd_64553.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the human DCAF2-DDB1 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-2.7822933 - 4.2695904
Average (Standard dev.)-0.0011339476 (±0.121247776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map-A

Fileemd_64553_half_map_1.map
AnnotationHalf-map-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map-B

Fileemd_64553_half_map_2.map
AnnotationHalf-map-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the human DCAF2-DDB1 complex

EntireName: Structure of the human DCAF2-DDB1 complex
Components
  • Complex: Structure of the human DCAF2-DDB1 complex
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Denticleless protein homolog

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Supramolecule #1: Structure of the human DCAF2-DDB1 complex

SupramoleculeName: Structure of the human DCAF2-DDB1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.319852 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHSSG RENLYFQGHM SYNYVVTAQK PTAVNGCVTG HFTSAEDLNL LIAKNTRLEI YVVTAEGLRP VKEVGMYGKI AVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF K VIPLDRDN ...String:
MHHHHHHSSG RENLYFQGHM SYNYVVTAQK PTAVNGCVTG HFTSAEDLNL LIAKNTRLEI YVVTAEGLRP VKEVGMYGKI AVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF K VIPLDRDN KELKAFNIRL EELHVIDVKF LYGCQAPTIC FVYQDPQGRH VKTYEVSLRE KEFNKGPWKQ ENVEAEASMV IA VPEPFGG AIIIGQESIT YHNGDKYLAI APPIIKQSTI VCHNRVDPNG SRYLLGDMEG RLFMLLLEKE EQMDGTVTLK DLR VELLGE TSIAECLTYL DNGVVFVGSR LGDSQLVKLN VDSNAQGSYV VAMETFTNLG PIVDMCVVDL ERQGQGQLVT CSGA FKEGS LRIIRNGIGI HEHASIDLPG IKGLWPLRSD PNRETDDTLV LSFVGQTRVL MLNGEEVEET ELMGFVDDQQ TFFCG NVAH QQLIQITSAS VRLVSQEPKA LVSEWKEPQA KNISVASCNS SQVVVAVGRA LYYLQIHPQE LRQISHTEME HEVACL DIT PLGDSNGLSP LCAIGLWTDI SARILKLPSF ELLHKEMLGG EIIPRSILMT TFESSHYLLC ALGDGALFYF GLNIETG LL SDRKKVTLGT QPTVLRTFRS LSTTNVFACS DRPTVIYSSN HKLVFSNVNL KEVNYMCPLN SDGYPDSLAL ANNSTLTI G TIDEIQKLHI RTVPLYESPR KICYQEVSQC FGVLSSRIEV QDTSGGTTAL RPSASTQALS SSVSSSKLFS SSTAPHETS FGEEVEVHNL LIIDQHTFEV LHAHQFLQNE YALSLVSCKL GKDPNTYFIV GTAMVYPAEA EPKQGRIVVF QYSDGKLQTV AEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG N FEEIARDF NPNWMSAVEI LDDDNFLGAE NAFNLFVCQK DSAATTDEER QHLQEVGLFH LGEFVNVFCH GSLVMQNLGE TS TPTQGSV LFGTVNGMIG LVTSLSESWY NLLLDMQNRL NKVIKSVGKI EHSFWRSFHT ERKTEPATGF IDGDLIESFL DIS RPKMQE VVANLQYDDG SGMKREATAD DLIKVVEELT RIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #2: Denticleless protein homolog

MacromoleculeName: Denticleless protein homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 79.506695 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLFNSVLRQP QLGVLRNGWS SQYPLQSLLT GYQCSGNDEH TSYGETGVPV PPFGCTFSSA PNMEHVLAVA NEEGFVRLYN TESQSFRKK CFKEWMAHWN AVFDLAWVPG ELKLVTAAGD QTAKFWDVKA GELIGTCKGH QCSLKSVAFS KFEKAVFCTG G RDGNIMVW ...String:
MLFNSVLRQP QLGVLRNGWS SQYPLQSLLT GYQCSGNDEH TSYGETGVPV PPFGCTFSSA PNMEHVLAVA NEEGFVRLYN TESQSFRKK CFKEWMAHWN AVFDLAWVPG ELKLVTAAGD QTAKFWDVKA GELIGTCKGH QCSLKSVAFS KFEKAVFCTG G RDGNIMVW DTRCNKKDGF YRQVNQISGA HNTSDKQTPS KPKKKQNSKG LAPSVDFQQS VTVVLFQDEN TLVSAGAVDG II KVWDLRK NYTAYRQEPI ASKSFLYPGS STRALGYSSL ILDSTGSTLF ANCTDDNIYM FNMTGLKTSP VAIFNGHQNS TFY VKSSLS PDDQFLVSGS SDEAAYIWKV STPWQPPTVL LGHSQEVTSV CWCPSDFTKI ATCSDDNTLK IWRLNRGLEE KPGG DKLST VGWASQKKKE SRPGLVTVTS SQSTPAKAPR AKCNPSNSSP SSAACAPSCA GDLPLPSNTP TFSIKTSPAK ARSPI NRRG SVSSVSPKPP SSFKMSIRNW VTRTPSSSPP ITPPASETKI MSPRKALIPV SQKSSQAEAC SESRNRVKRR LDSSCL ESV KQKCVKSCNC VTELDGQVEN LHLDLCCLAG NQEDLSKDSL GPTKSSKIEG AGTSISEPPS PISPYASESC GTLPLPL RP CGEGSEMVGK ENSSPENKNW LLAMAAKRKA ENPSPRSPSS QTPNSRRQSG KKLPSPVTIT PSSMRKICTY FHRKSQED F CGPEHSTEL

UniProtKB: Denticleless protein homolog

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration1.45 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClsodium chloride
0.5 mMTCEPtris(2-carboxyethyl) phosphine
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7822362
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8tl6


Details: The predicted models of human DCAF2 were downloaded from the AlphaFold Protein Structure Database (https://www.alphafold.ebi.ac.uk/entry/Q9NZJ0).
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 7822362
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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