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- PDB-7bqu: Cereblon in complex with SALL4 and (S)-thalidomide -

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Basic information

Entry
Database: PDB / ID: 7bqu
TitleCereblon in complex with SALL4 and (S)-thalidomide
Components
  • Protein cereblon
  • Sal-like protein 4
KeywordsMETAL BINDING PROTEIN / ZINC FINGER / E3 UBIQUITIN LIGASE / COMPLEX / THALIDOMIDE
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / negative regulation of monoatomic ion transmembrane transport / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / Cul4A-RING E3 ubiquitin ligase complex / inner cell mass cell proliferation / ventricular septum development / locomotory exploration behavior / somatic stem cell population maintenance / positive regulation of Wnt signaling pathway ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / negative regulation of monoatomic ion transmembrane transport / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / Cul4A-RING E3 ubiquitin ligase complex / inner cell mass cell proliferation / ventricular septum development / locomotory exploration behavior / somatic stem cell population maintenance / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / Potential therapeutics for SARS / protein ubiquitination / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / 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 protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
S-Thalidomide / Protein cereblon / Sal-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFurihata, H. / Miyauchi, Y. / Asano, A. / Tanokura, M. / Miyakawa, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19am0101077 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide.
Authors: Furihata, H. / Yamanaka, S. / Honda, T. / Miyauchi, Y. / Asano, A. / Shibata, N. / Tanokura, M. / Sawasaki, T. / Miyakawa, T.
History
DepositionMar 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein cereblon
B: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1345
Polymers15,7452
Non-polymers3893
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.962, 92.718, 43.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

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Components

#1: Protein Protein cereblon


Mass: 12614.542 Da / Num. of mol.: 1
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: Protein/peptide Sal-like protein 4 / Zinc finger protein 797 / Zinc finger protein SALL4


Mass: 3130.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SALL4, ZNF797 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJQ4
#3: Chemical ChemComp-EF2 / S-Thalidomide / Thalidomide


Mass: 258.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 27% PEG 4000, 0.1 M sodium acetate (pH 5.5), 0.1 M magnesium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.99 Å / Num. obs: 11808 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 24.39 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.044 / Rrim(I) all: 0.158 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 746 / CC1/2: 0.826 / Rpim(I) all: 0.363 / Rrim(I) all: 1.31 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXVer 1.15.1_3469refinement
XDSdata reduction
Aimlessdata scaling
PHASERVer 1.15.1_3469phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZ4, 5YJ0
Resolution: 1.9→34.674 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.81
RfactorNum. reflection% reflection
Rfree0.2358 561 4.76 %
Rwork0.1908 --
obs0.1929 11790 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→34.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 21 48 1119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111102
X-RAY DIFFRACTIONf_angle_d1.3751497
X-RAY DIFFRACTIONf_dihedral_angle_d7.452635
X-RAY DIFFRACTIONf_chiral_restr0.046163
X-RAY DIFFRACTIONf_plane_restr0.011182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.09130.22831300.22032782X-RAY DIFFRACTION100
2.0913-2.39380.23851380.20992748X-RAY DIFFRACTION100
2.3938-3.01570.25531490.21342780X-RAY DIFFRACTION100
3.0157-34.6740.22691440.16972919X-RAY DIFFRACTION100

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