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- PDB-9hne: Cereblon in complex with DDB1, GSPT1 and Compound-1 -

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Basic information

Entry
Database: PDB / ID: 9hne
TitleCereblon in complex with DDB1, GSPT1 and Compound-1
Components
  • DNA damage-binding protein 1
  • Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
  • Protein cereblon
KeywordsONCOPROTEIN / CRBN / GSPT1 / TPD / Molecular glue
Function / homology
Function and homology information


translation release factor complex / negative regulation of monoatomic ion transmembrane transport / regulation of translational termination / protein methylation / positive regulation by virus of viral protein levels in host cell / translation release factor activity / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...translation release factor complex / negative regulation of monoatomic ion transmembrane transport / regulation of translational termination / protein methylation / positive regulation by virus of viral protein levels in host cell / translation release factor activity / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-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 / locomotory exploration behavior / cullin family protein binding / viral release from host cell / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / proteasomal protein catabolic process / translational termination / positive regulation of gluconeogenesis / cytosolic ribosome / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / G1/S transition of mitotic cell cycle / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Wnt signaling pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transmembrane transporter binding / chromosome, telomeric region / protein ubiquitination / translation / DNA repair / GTPase activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / GTP binding / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / extracellular space / DNA binding / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / GTP-eEF1A C-terminal domain-like / 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 ...: / GTP-eEF1A C-terminal domain-like / 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 / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / PUA-like superfamily / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Eukaryotic peptide chain release factor GTP-binding subunit ERF3A / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsKlejnot, M. / Walczak, M.J.
Funding support Poland, 1items
OrganizationGrant numberCountry
Other private Poland
CitationJournal: Commun Chem / Year: 2025
Title: Targeted degradation of GSPT1 and NEK7 by a molecular glue prodrug for treatment of HCC.
Authors: Glaza, P. / Pluta, R. / Odrzywol, K.E. / Klejnot, M. / Wieczorek, M. / Cottens, S. / Coppen, D. / Dobrzanski, P. / Drmota, T. / Lis-Grzesniak, J. / Sniezewska, A. / Majkut, J. / Mianowska, M. ...Authors: Glaza, P. / Pluta, R. / Odrzywol, K.E. / Klejnot, M. / Wieczorek, M. / Cottens, S. / Coppen, D. / Dobrzanski, P. / Drmota, T. / Lis-Grzesniak, J. / Sniezewska, A. / Majkut, J. / Mianowska, M. / Rozborska, P. / Jarmuszkiewicz, M. / Kaczanowska, K. / Adamska, A. / Takagi, T. / Sawicka, A. / Serwotka-Suszczak, A. / Makowska, O. / Gajewska, D. / Jurczak, K. / Leszkowicz, K. / Mankiewicz, M. / Przytulski, K. / Wisniewski, J. / Szlachcic, A. / Walczak, M.J.
History
DepositionDec 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
B: DNA damage-binding protein 1
C: Protein cereblon
D: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
E: DNA damage-binding protein 1
F: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,45810
Polymers390,7156
Non-polymers7434
Water00
1
A: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
B: DNA damage-binding protein 1
C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7295
Polymers195,3573
Non-polymers3722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
E: DNA damage-binding protein 1
F: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7295
Polymers195,3573
Non-polymers3722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.340, 112.380, 177.940
Angle α, β, γ (deg.)90.00, 95.25, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Eukaryotic peptide chain release factor GTP-binding subunit ERF3A / Eukaryotic peptide chain release factor subunit 3a / eRF3a / G1 to S phase transition protein 1 homolog


Mass: 21851.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSPT1, ERF3A / Production host: Escherichia coli (E. coli)
References: UniProt: P15170, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: unidentified baculovirus / References: UniProt: Q16531
#3: Protein Protein cereblon


Mass: 46408.320 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: unidentified baculovirus / References: UniProt: Q96SW2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-A1IWG / 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid


Mass: 306.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11FN2O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 4.03 Å3/Da / Density % sol: 69.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 3.9→49.49 Å / Num. obs: 55075 / % possible obs: 96.5 % / Redundancy: 4.44 % / CC1/2: 0.978 / Net I/σ(I): 5.06
Reflection shellResolution: 3.9→4.14 Å / Mean I/σ(I) obs: 1.11 / Num. unique obs: 8852 / CC1/2: 0.483 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→49.49 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.796 / SU B: 82.281 / SU ML: 1.078 / Cross valid method: THROUGHOUT / ESU R Free: 0.941 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.33557 2100 3.8 %RANDOM
Rwork0.25949 ---
obs0.26245 52973 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 134.396 Å2
Baniso -1Baniso -2Baniso -3
1-6.97 Å2-0 Å22.29 Å2
2---6.65 Å2-0 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 3.9→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25975 0 46 0 26021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01226498
X-RAY DIFFRACTIONr_bond_other_d0.0010.01625551
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.82935857
X-RAY DIFFRACTIONr_angle_other_deg0.4711.75758917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.41253250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.3855.408147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.078104751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.24131
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0230603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025829
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.36713.05713126
X-RAY DIFFRACTIONr_mcbond_other10.36713.05713126
X-RAY DIFFRACTIONr_mcangle_it17.48123.41716334
X-RAY DIFFRACTIONr_mcangle_other17.4823.41716335
X-RAY DIFFRACTIONr_scbond_it8.82813.98113372
X-RAY DIFFRACTIONr_scbond_other8.82713.9813373
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.84225.42419524
X-RAY DIFFRACTIONr_long_range_B_refined24.873122.6528392
X-RAY DIFFRACTIONr_long_range_B_other24.873122.6528393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.901→4.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 153 -
Rwork0.374 3874 -
obs--97.34 %

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