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- EMDB-41105: CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3 -

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Basic information

Entry
Database: EMDB / ID: EMD-41105
TitleCryoEM structure of human DDB1-DCAF12 in complex with MAGEA3
Map datathe CryoEM map
Sample
  • Complex: Ternary complex of DCAF12-DDB1-MAGEA3
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 12
    • Protein or peptide: Melanoma-associated antigen 3
KeywordsDCAF12 / DNA damage-binding protein 1 / DDB1 / E3 ligase / LIGASE
Function / homology
Function and homology information


caspase binding / positive regulation by virus of viral protein levels in host cell / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / negative regulation of protein processing / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition ...caspase binding / positive regulation by virus of viral protein levels in host cell / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / negative regulation of protein processing / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-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 / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of gluconeogenesis / T cell activation / negative regulation of autophagy / regulation of autophagy / proteasomal protein catabolic process / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / histone deacetylase binding / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / DNA repair / centrosome / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Melanoma-associated antigen 3 / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsDuda D / Righetto G / Li Y / Loppnau P / Seitova A / Santhakumar V / Halabelian L / Yin Y
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3
Authors: Duda D / Righetto G / Li Y / Loppnau P / Seitova A / Santhakumar V / Halabelian L / Yin Y
History
DepositionJun 23, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41105.png

Downloads & links

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Map

FileDownload / File: emd_41105.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe CryoEM map
Voxel sizeX=Y=Z: 0.948 Å
Density
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.13106275 - 0.36165443
Average (Standard dev.)0.00025417775 (±0.014357673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 242.688 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41105_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41105_half_map_2.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 DCAF12-DDB1-MAGEA3

EntireName: Ternary complex of DCAF12-DDB1-MAGEA3
Components
  • Complex: Ternary complex of DCAF12-DDB1-MAGEA3
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 12
    • Protein or peptide: Melanoma-associated antigen 3

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Supramolecule #1: Ternary complex of DCAF12-DDB1-MAGEA3

SupramoleculeName: Ternary complex of DCAF12-DDB1-MAGEA3 / 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: 127.097469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK ...String:
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRNGIGI HEHA SIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFCGNVAH QQLIQITSAS VRLVS QEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVACLDIT PLGDSNGLSP LCAIGL WTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIETGLL SDRKKVTLGT QPTVLRT FR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLTIG TIDEIQKLHI RTVPLYES P RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHETS FGEEVEVHNL LIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME GNFEEIARDF NPNWMSAVEI L DDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ETSTPTQGSV LFGTVNGMIG LV TSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGM KREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #2: DDB1- and CUL4-associated factor 12

MacromoleculeName: DDB1- and CUL4-associated factor 12 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.760512 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHSSG RENLYFQGMA RKVVSRKRKA PASPGAGSDA QGPQFGWDHS LHKRKRLPPV KRSLVYYLKN REVRLQNETS YSRVLHGYA AQQLPSLLKE REFHLGTLNK VFASQWLNHR QVVCGTKCNT LFVVDVQTSQ ITKIPILKDQ EPGGVTQQGC G IHAIELNP ...String:
MHHHHHHSSG RENLYFQGMA RKVVSRKRKA PASPGAGSDA QGPQFGWDHS LHKRKRLPPV KRSLVYYLKN REVRLQNETS YSRVLHGYA AQQLPSLLKE REFHLGTLNK VFASQWLNHR QVVCGTKCNT LFVVDVQTSQ ITKIPILKDQ EPGGVTQQGC G IHAIELNP SRTLLATGGD NPNSLAIYRL PTLDPVCVGD DGHKDWIFSI AWISDTMAVS GSRDGSMGLW EVTDDVLTKS DA RHNVSRV PVYAHITHKA LKDIPKEDTN PDNCKVRALA FNNKNKELGA VSLDGYFHLW KAENTLSKLL STKLPYCREN VCL AYGSEW SVYAVGSQAH VSFLDPRQPS YNVKSVCSRE RGSGIRSVSF YEHIITVGTG QGSLLFYDIR AQRFLEERLS ACYG SKPRL AGENLKLTTG KGWLNHDETW RNYFSDIDFF PNAVYTHCYD SSGTKLFVAG GPLPSGLHGN YAGLWS

UniProtKB: DDB1- and CUL4-associated factor 12

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Macromolecule #3: Melanoma-associated antigen 3

MacromoleculeName: Melanoma-associated antigen 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.03276 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEFQAALSRK VAELVHFLLL KYRAREPVTK AEMLGSVVGN WQYFFPVIFS KASSSLQLVF GIELMEVDPI GHLYIFATCL GLSYDGLLG DNQIMPKAGL LIIVLAIIAR EGDCAPEEKI WEELSVLEVF EGREDSILGD PKKLLTQHFV QENYLEYRQV P GSDPACYE ...String:
MEFQAALSRK VAELVHFLLL KYRAREPVTK AEMLGSVVGN WQYFFPVIFS KASSSLQLVF GIELMEVDPI GHLYIFATCL GLSYDGLLG DNQIMPKAGL LIIVLAIIAR EGDCAPEEKI WEELSVLEVF EGREDSILGD PKKLLTQHFV QENYLEYRQV P GSDPACYE FLWGPRALVE TSYVKVLHHM VKISGGPHIS YPPLHEWVLR EGEE

UniProtKB: Melanoma-associated antigen 3

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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

Concentration0.2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 476215

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