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- EMDB-54644: Locally refined map of CRBN TBD bound to spirocyclic ligand in th... -

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Basic information

Entry
Database: EMDB / ID: EMD-54644
TitleLocally refined map of CRBN TBD bound to spirocyclic ligand in the open conformation
Map dataSharpened focused map
Sample
  • Complex: Complex of CRL4 E3 adapter-receptor pair DDB1 and CRBN bound to spirocyclic ligand
    • Protein or peptide: Cereblon
KeywordsE3 ubiquitin ligase / LIGASE
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / locomotory exploration behavior / Cul4A-RING E3 ubiquitin ligase complex / limb development / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding ...negative regulation of monoatomic ion transmembrane transport / locomotory exploration behavior / Cul4A-RING E3 ubiquitin ligase complex / limb development / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination / perinuclear region of cytoplasm / membrane / metal ion binding / 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) / PUA-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 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
DepositionAug 4, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54644.png

Downloads & links

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Map

FileDownload / File: emd_54644.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened focused map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 360 pix.
= 269.64 Å		0.75 Å/pix.
x 360 pix.
= 269.64 Å		0.75 Å/pix.
x 360 pix.
= 269.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.749 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.1380906 - 1.5040299
Average (Standard dev.)-0.000036753318 (±0.009648211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 269.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54644_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened focused map

Fileemd_54644_additional_1.map
AnnotationUnsharpened focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused half map A

Fileemd_54644_half_map_1.map
AnnotationFocused half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54644_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 : 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: 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
Details: Locally refined map of CRBN thalidomide binding domain bound to spirocyclic ligand
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 143.77612 KDa

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Macromolecule #1: Cereblon

MacromoleculeName: Cereblon / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAGEGDQQDA AHNMGNHLPL LPAESEEEDE MEVEDQDSKE AKKPNIINFD TSLPTSHTYL GADMEEFHGR TLHDDDSCQV IPVLPQVMM ILIPGQTLPL QLFHPQEVSM VRNLIQKDRT FAVLAYSNVQ EREAQFGTTA EIYAYREEQD FGIEIVKVKA I GRQRFKVL ...String:
MAGEGDQQDA 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 GETLTVYKAC 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

Concentration7.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
200.0 mMsodium chlorideNaCl
0.25 mMtris(2-carboxyethyl)phosphine
0.011 %Lauryl Maltose-Neopentyl Glycol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k 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: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Version: 4.6.2 / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 195995
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 modelPDB ID:

8cvp


Chain - Source name: PDB / Chain - Initial model type: experimental model
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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