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- PDB-5v3o: Cereblon in complex with DDB1 and CC-220 -

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Basic information

Entry
Database: PDB / ID: 5v3o
TitleCereblon in complex with DDB1 and CC-220
Components
  • DNA damage-binding protein 1
  • Protein cereblon
KeywordsLIGASE / E3 / ubiquitin ligase / CRL4 / DCAF
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex ...negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-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 / positive regulation of Wnt signaling pathway / viral release from host cell / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / positive regulation of gluconeogenesis / proteasomal protein catabolic process / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / positive regulation of protein-containing complex assembly / 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 / Wnt signaling pathway / Formation of Incision Complex in GG-NER / 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 / protein-macromolecule adaptor activity / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Peptide methionine sulfoxide reductase. / DNA polymerase; domain 1 - #910 / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / CULT domain / CULT domain profile. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Peptide methionine sulfoxide reductase. / DNA polymerase; domain 1 - #910 / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / 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) / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / PUA-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Beta Complex / DNA polymerase; domain 1 / Roll / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-8W7 / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsMatyskiela, M. / Pagarigan, B. / Chamberlain, P.
CitationJournal: J. Med. Chem. / Year: 2018
Title: A Cereblon Modulator (CC-220) with Improved Degradation of Ikaros and Aiolos.
Authors: Matyskiela, M.E. / Zhang, W. / Man, H.W. / Muller, G. / Khambatta, G. / Baculi, F. / Hickman, M. / LeBrun, L. / Pagarigan, B. / Carmel, G. / Lu, C.C. / Lu, G. / Riley, M. / Satoh, Y. / ...Authors: Matyskiela, M.E. / Zhang, W. / Man, H.W. / Muller, G. / Khambatta, G. / Baculi, F. / Hickman, M. / LeBrun, L. / Pagarigan, B. / Carmel, G. / Lu, C.C. / Lu, G. / Riley, M. / Satoh, Y. / Schafer, P. / Daniel, T.O. / Carmichael, J. / Cathers, B.E. / Chamberlain, P.P.
History
DepositionMar 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-binding protein 1
C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,2094
Polymers173,6942
Non-polymers5152
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-27 kcal/mol
Surface area59150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.029, 126.886, 172.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein Protein cereblon


Mass: 46596.566 Da / Num. of mol.: 1 / Fragment: residues 40-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#3: Chemical ChemComp-8W7 / (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione


Mass: 449.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27N3O5
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200mM NaCl, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.2→50.01 Å / Num. obs: 40911 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 3.2→50.01 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.88 / SU B: 41.998 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26733 2023 5 %RANDOM
Rwork0.20381 ---
obs0.20693 38828 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 3.2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11141 0 34 0 11175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911423
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210793
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9615519
X-RAY DIFFRACTIONr_angle_other_deg2.0682.99824721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4351438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67824.509479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.582151885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1171554
X-RAY DIFFRACTIONr_chiral_restr0.0810.21806
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112897
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022546
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_it3.0017.8025800
X-RAY DIFFRACTIONr_mcbond_other2.9997.8015799
X-RAY DIFFRACTIONr_mcangle_it5.14211.6947222
X-RAY DIFFRACTIONr_mcangle_other5.14211.6957223
X-RAY DIFFRACTIONr_scbond_it2.6668.0385623
X-RAY DIFFRACTIONr_scbond_other2.6678.0385622
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.63211.9628298
X-RAY DIFFRACTIONr_long_range_B_refined7.57160.33611676
X-RAY DIFFRACTIONr_long_range_B_other7.57160.33711677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 151 -
Rwork0.278 2766 -
obs--99.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.94730.6573-0.72890.9759-0.67080.6219-0.15490.18290.0060.06550.0678-0.15090.0995-0.12670.08710.1915-0.10360.00920.23620.03940.176933.362841.9836-41.43
20.42270.2888-0.92980.2134-0.69942.3797-0.0346-0.12740.0987-0.0131-0.02530.02290.09260.13820.05980.21860.0113-0.0870.1705-0.08240.25536.557948.454-20.4681
30.9531-0.18820.86760.9226-0.25140.9337-0.2649-0.05260.20590.0833-0.11150.127-0.1631-0.05530.37630.15680.050.03820.1297-0.13240.4093-51.967312.4682-21.7473
40.21460.00480.12190.28100.3914-0.1067-0.0775-0.0075-0.10730.14250.00990.00660.0735-0.03580.2937-0.02580.04980.1739-0.05510.0953-1.7316.0981-23.512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C249 - 428
2X-RAY DIFFRACTION2C47 - 186
3X-RAY DIFFRACTION3A392 - 709
4X-RAY DIFFRACTION4A2 - 391
5X-RAY DIFFRACTION4A710 - 1140

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