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- PDB-9gy3: Crystal structure of CRBNmidi in complex with (S)-dHTC1 -

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Basic information

Entry
Database: PDB / ID: 9gy3
TitleCrystal structure of CRBNmidi in complex with (S)-dHTC1
ComponentsProtein cereblon
KeywordsLIGASE / E3 Ligase / TPD / molecular glue / induced proximity
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / protein ubiquitination ...negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / protein ubiquitination / perinuclear region of cytoplasm / metal ion binding / nucleus / membrane / 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
: / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRutter, Z.J. / Shaum, J.B. / Ciulli, A. / Erb, M.A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Biorxiv / Year: 2025
Title: High-throughput diversification of protein-ligand surfaces to discover chemical inducers of proximity.
Authors: Shaum, J.B. / Munoz I Ordono, M. / Steen, E.A. / Wenge, D.V. / Cheong, H. / Hunkeler, M. / Bilotta, E.M. / Rutter, Z. / Barta, P.A. / Thornhill, A.M. / Milosevich, N. / Hargis, L.M. / ...Authors: Shaum, J.B. / Munoz I Ordono, M. / Steen, E.A. / Wenge, D.V. / Cheong, H. / Hunkeler, M. / Bilotta, E.M. / Rutter, Z. / Barta, P.A. / Thornhill, A.M. / Milosevich, N. / Hargis, L.M. / Janowski, J. / Bishop, T.R. / Carter, T.R. / da Camara, B. / Hinterndorfer, M. / Dada, L. / He, W.J. / Offensperger, F. / Furihata, H. / Schweber, S.R. / Hatton, C. / Wen, Y. / Cravatt, B.F. / Engle, K.M. / Donovan, K.A. / Melillo, B. / Kitamura, S. / Ciulli, A. / Armstrong, S.A. / Fischer, E.S. / Winter, G.E. / Erb, M.A.
History
DepositionOct 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein cereblon
C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4426
Polymers74,9582
Non-polymers1,4844
Water1,20767
1
A: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2213
Polymers37,4791
Non-polymers7422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2213
Polymers37,4791
Non-polymers7422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.501, 53.501, 236.121
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Protein cereblon


Mass: 37478.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SW2
#2: Chemical ChemComp-A1IQT / 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide


Mass: 676.786 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N8O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus H10 (0.1 M Buffer System 3 pH 8.5, 0.12 M Alcohols, 30 % Precipitant Mix 2) (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: May 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 2.5→236.12 Å / Num. obs: 26206 / % possible obs: 98.3 % / Redundancy: 10.7 % / Biso Wilson estimate: 51.55 Å2 / CC1/2: 0.969 / Net I/σ(I): 3.5
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 2917 / CC1/2: 0.182

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158-000refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.13 Å / SU ML: 0.4675 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3032 1238 4.82 %
Rwork0.2437 24452 -
obs0.2465 25690 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.77 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5075 0 98 67 5240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245293
X-RAY DIFFRACTIONf_angle_d0.56457198
X-RAY DIFFRACTIONf_chiral_restr0.0433804
X-RAY DIFFRACTIONf_plane_restr0.0042923
X-RAY DIFFRACTIONf_dihedral_angle_d8.2082748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.3907800.37772494X-RAY DIFFRACTION89.75
2.6-2.720.35271510.36252683X-RAY DIFFRACTION96.04
2.72-2.860.36891500.32192709X-RAY DIFFRACTION99.76
2.86-3.040.40261180.34132776X-RAY DIFFRACTION99.86
3.04-3.280.36621300.29812798X-RAY DIFFRACTION99.93
3.28-3.60.32531660.23582738X-RAY DIFFRACTION100
3.61-4.130.29441720.2312736X-RAY DIFFRACTION100
4.13-5.20.24851460.18832763X-RAY DIFFRACTION99.97
5.2-43.130.25591250.19312755X-RAY DIFFRACTION99.17

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