[English] 日本語
Yorodumi
- EMDB-41105: CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3 -

+
Open data


ID or keywords:

Loading...

-
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 / viral release from host cell / ectopic germ cell programmed cell death / ubiquitin-like ligase-substrate adaptor activity / positive regulation of viral genome replication / proteasomal protein catabolic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of gluconeogenesis / negative regulation of autophagy / T cell activation / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / histone deacetylase binding / 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 / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / regulation of autophagy / protein ubiquitination / DNA repair / apoptotic process / centrosome / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / 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
: / : / DDB1- and CUL4-associated factor 12 beta propeller / 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 ...: / : / DDB1- and CUL4-associated factor 12 beta propeller / 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 / 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 / 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
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: PNAS Nexus / Year: 2024
Title: Probing the CRL4 interactions with MAGEA3 and CCT5 di-Glu C-terminal degrons.
Authors: Germanna Lima Righetto / Yanting Yin / David M Duda / Victoria Vu / Magdalena M Szewczyk / Hong Zeng / Yanjun Li / Peter Loppnau / Tony Mei / Yen-Yen Li / Alma Seitova / Aaron N Patrick / ...Authors: Germanna Lima Righetto / Yanting Yin / David M Duda / Victoria Vu / Magdalena M Szewczyk / Hong Zeng / Yanjun Li / Peter Loppnau / Tony Mei / Yen-Yen Li / Alma Seitova / Aaron N Patrick / Jean-Francois Brazeau / Charu Chaudhry / Dalia Barsyte-Lovejoy / Vijayaratnam Santhakumar / Levon Halabelian /
Abstract: Damaged DNA-binding protein-1 (DDB1)- and CUL4-associated factor 12 (DCAF12) serves as the substrate recognition component within the Cullin4-RING E3 ligase (CRL4) complex, capable of identifying C- ...Damaged DNA-binding protein-1 (DDB1)- and CUL4-associated factor 12 (DCAF12) serves as the substrate recognition component within the Cullin4-RING E3 ligase (CRL4) complex, capable of identifying C-terminal double-glutamic acid degrons to promote the degradation of specific substrates through the ubiquitin proteasome system. Melanoma-associated antigen 3 (MAGEA3) and T-complex protein 1 subunit epsilon (CCT5) proteins have been identified as cellular targets of DCAF12. To further characterize the interactions between DCAF12 and both MAGEA3 and CCT5, we developed a suite of biophysical and proximity-based cellular NanoBRET assays showing that the C-terminal degron peptides of both MAGEA3 and CCT5 form nanomolar affinity interactions with DCAF12 in vitro and in cells. Furthermore, we report here the 3.17 Å cryo-EM structure of DDB1-DCAF12-MAGEA3 complex revealing the key DCAF12 residues responsible for C-terminal degron recognition and binding. Our study provides new insights and tools to enable the discovery of small molecule handles targeting the WD40-repeat domain of DCAF12 for future proteolysis targeting chimera design and development.
History
DepositionJun 23, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41105.png

Downloads & links

-
Map

FileDownload / File: emd_41105.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe CryoEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 242.688 Å		0.95 Å/pix.
x 256 pix.
= 242.688 Å		0.95 Å/pix.
x 256 pix.
= 242.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.948 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
Half map: #2

Fileemd_41105_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41105_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.0 e/Å2
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 processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more