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- EMDB-55057: Consensus map of CRBN bound to dihydrouracil ligand in the closed... -

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Basic information

Entry
Database: EMDB / ID: EMD-55057
TitleConsensus map of CRBN bound to dihydrouracil ligand in the closed conformation
Map data
Sample
  • Complex: Complex of CRL4 E3 adapter-receptor pair DDB1 and CRBN bound to spirocyclic ligand
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Cereblon
KeywordsE3 ubiquitin ligase / LIGASE
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / 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 cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation ...negative regulation of monoatomic ion transmembrane transport / 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 cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / WD40-repeat domain binding / nucleotide-excision repair complex / locomotory exploration behavior / regulation of cell cycle phase transition / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / Cul4B-RING E3 ubiquitin ligase complex / regulation of cellular response to stress / limb development / viral release from host cell / cullin family protein binding / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / regulation of DNA-templated DNA replication initiation / positive regulation of viral genome replication / positive regulation of gluconeogenesis / regulation of embryonic development / replication fork processing / proteasomal protein catabolic process / epigenetic regulation of gene expression / positive regulation of protein-containing complex assembly / nucleotide-excision repair / regulation of autophagy / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / cell population proliferation / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / cellular response to UV / positive regulation of protein catabolic process / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / site of double-strand break / regulation of cell population proliferation / Neddylation / spermatogenesis / ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / transmembrane transporter binding / chromosome, telomeric region / protein-macromolecule adaptor activity / protein ubiquitination / DNA repair / DNA damage response / nucleolus / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular exosome / nucleoplasm / extracellular region / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / : ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / : / 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 / PUA-like superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsCowan AD / Rutter ZJ / McAulay K / Ciulli A
Funding support Germany, 1 items
OrganizationGrant numberCountry
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Protein Sci / Year: 2023
Title: UCSF ChimeraX: Tools for structure building and analysis.
Authors: Elaine C Meng / Thomas D Goddard / Eric F Pettersen / Greg S Couch / Zach J Pearson / John H Morris / Thomas E Ferrin /
Abstract: Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at challenging resolutions of 3-4 Å. We ...Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at challenging resolutions of 3-4 Å. We describe new methods in the UCSF ChimeraX molecular modeling package that take advantage of machine-learning structure predictions, provide likelihood-based fitting in maps, and compute per-residue scores to identify modeling errors. Additional model-building tools assist analysis of mutations, post-translational modifications, and interactions with ligands. We present the latest ChimeraX model-building capabilities, including several community-developed extensions. ChimeraX is available free of charge for noncommercial use at https://www.rbvi.ucsf.edu/chimerax.
History
DepositionSep 12, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55057.png

Downloads & links

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Map

FileDownload / File: emd_55057.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 360 pix.
= 255.6 Å		0.71 Å/pix.
x 360 pix.
= 255.6 Å		0.71 Å/pix.
x 360 pix.
= 255.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0134
Minimum - Maximum-0.11050498 - 0.18769191
Average (Standard dev.)-0.00000459331 (±0.0038576813)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 255.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55057_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_55057_additional_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55057_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_55057_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of CRL4 E3 adapter-receptor pair DDB1 and CRBN bound to s...

EntireName: Complex of CRL4 E3 adapter-receptor pair DDB1 and CRBN bound to spirocyclic ligand
Components
  • Complex: Complex of CRL4 E3 adapter-receptor pair DDB1 and CRBN bound to spirocyclic ligand
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Cereblon

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Supramolecule #1: Complex of CRL4 E3 adapter-receptor pair DDB1 and CRBN bound to s...

SupramoleculeName: Complex of CRL4 E3 adapter-receptor pair DDB1 and CRBN bound to spirocyclic ligand
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 143.77612 KDa

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 LRIIRNGIGG NGNS GEIQK LHIRTVPLYE SPRKICYQEV SQCFGVLSSR IEVQDTSGGT TALRPSASTQ ALSSSVSSSK LFSSSTAPHE TSFGE EVEV HNLLIIDQHT FEVLHAHQFL QNEYALSLVS CKLGKDPNTY FIVGTAMVYP EEAEPKQGRI VVFQYSDGKL QTVAEK EVK GAVYSMVEFN GKLLASINST VRLYEWTTEK ELRTECNHYN NIMALYLKTK GDFILVGDLM RSVLLLAYKP MEGNFEE IA RDFNPNWMSA VEILDDDNFL GAENAFNLFV CQKDSAATTD EERQHLQEVG LFHLGEFVNV FCHGSLVMQN LGETSTPT Q GSVLFGTVNG MIGLVTSLSE SWYNLLLDMQ NRLNKVIKSV GKIEHSFWRS FHTERKTEPA TGFIDGDLIE SFLDISRPK MQEVVANLQY DDGSGMKREA TADDLIKVVE ELTRIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #2: Cereblon

MacromoleculeName: Cereblon / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SAGEGDQQDA AHNMGNHLPL LPAESEEEDE MEVEDQDSKE AKKPNIINFD TSLPTSHTYL GADMEEFHGR TLHDDDSCQV IPVLPQVMM ILIPGQTLPL QLFHPQEVSM VRNLIQKDRT FAVLAYSNVQ EREAQFGTTA EIYAYREEQD FGIEIVKVKA I GRQRFKVL ...String:
SAGEGDQQDA AHNMGNHLPL LPAESEEEDE MEVEDQDSKE AKKPNIINFD TSLPTSHTYL GADMEEFHGR TLHDDDSCQV IPVLPQVMM ILIPGQTLPL QLFHPQEVSM VRNLIQKDRT FAVLAYSNVQ EREAQFGTTA EIYAYREEQD FGIEIVKVKA I GRQRFKVL ELRTQSDGIQ QAKVQILPEC VLPSTMSAVQ LESLNKCQIF PSKPVSREDQ CSYKWWQKYQ KRKFHCANLT SW PRWLYSL YDAETLMDRI KKQLREWDEN LKDDSLPSNP IDFSYRVAAC LPIDDVLRIQ LLKIGSAIQR LRCELDIMNK CTS LCCKQC QETEITTKNE IFSLSLCGPM AAYVNPHGYV HETLTVYKAC NLNLIGRPST EHSWFPGYAW TVAQCKICAS HIGW KFTAT KKDMSPQKFW GLTRSALLPT IPDTEDEISP DKVILCL

UniProtKB: Protein cereblon

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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

Concentration0.72 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHEPES
200.0 mMsodium chlorideNaCl
0.25 mMtris(2-carboxyethyl)phosphine
0.011 %Lauryl Maltose-Neopentyl Glycol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 35 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 3752 / Average electron dose: 21.94 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7)
Details: cryoSPARC non-uniform refinement was used for the final reconstruction of the consensus map, and cryoSPARC local refinement was used for the locally refined map of the LON and thalidomide binding domains
Number images used: 56510
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: Other, initial_model_type: experimental modelInitial model for CRBN LON, TBD and helical bundle was structure of CRBNmidi bound to dihrydrouracil ligand
source_name: PDB, initial_model_type: experimental modelDDB1 and DDB1 binding region of CRBN were used as intial model

8d81

DetailsInitial fitting was done in ChimeraX, followed by flexible fitting in Coot. The model was refined with iterative rounds of building in Coot and refinement in PHENIX real space refine
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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