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- PDB-7u8f: Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) an... -

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Basic information

Entry
Database: PDB / ID: 7u8f
TitleTernary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709
Components
  • DNA damage-binding protein 1
  • IKZF2
  • Protein cereblon
KeywordsLIGASE / molecular glue / targeted protein degradation
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / 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 / Cul4-RING E3 ubiquitin ligase complex ...negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / 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 / 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 / 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 / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / 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 / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transmembrane transporter binding / chromosome, telomeric region / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / DNA polymerase; domain 1 - #910 / 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 ...: / DNA polymerase; domain 1 - #910 / 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 / 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. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger C2H2-type / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-LWK / DNA damage-binding protein 1 / Uncharacterized protein ZNFN1A2 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsMa, X. / Ornelas, E. / Clifton, M.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Cell Chem Biol / Year: 2023
Title: Discovery and characterization of a selective IKZF2 glue degrader for cancer immunotherapy.
Authors: Bonazzi, S. / d'Hennezel, E. / Beckwith, R.E.J. / Xu, L. / Fazal, A. / Magracheva, A. / Ramesh, R. / Cernijenko, A. / Antonakos, B. / Bhang, H.C. / Caro, R.G. / Cobb, J.S. / Ornelas, E. / ...Authors: Bonazzi, S. / d'Hennezel, E. / Beckwith, R.E.J. / Xu, L. / Fazal, A. / Magracheva, A. / Ramesh, R. / Cernijenko, A. / Antonakos, B. / Bhang, H.C. / Caro, R.G. / Cobb, J.S. / Ornelas, E. / Ma, X. / Wartchow, C.A. / Clifton, M.C. / Forseth, R.R. / Fortnam, B.H. / Lu, H. / Csibi, A. / Tullai, J. / Carbonneau, S. / Thomsen, N.M. / Larrow, J. / Chie-Leon, B. / Hainzl, D. / Gu, Y. / Lu, D. / Meyer, M.J. / Alexander, D. / Kinyamu-Akunda, J. / Sabatos-Peyton, C.A. / Dales, N.A. / Zecri, F.J. / Jain, R.K. / Shulok, J. / Wang, Y.K. / Briner, K. / Porter, J.A. / Tallarico, J.A. / Engelman, J.A. / Dranoff, G. / Bradner, J.E. / Visser, M. / Solomon, J.M.
History
DepositionMar 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein cereblon
B: DNA damage-binding protein 1
C: IKZF2
D: Protein cereblon
E: DNA damage-binding protein 1
F: IKZF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,16221
Polymers286,0586
Non-polymers2,10315
Water34219
1
A: Protein cereblon
B: DNA damage-binding protein 1
C: IKZF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,96210
Polymers143,0293
Non-polymers9337
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Protein cereblon
E: DNA damage-binding protein 1
F: IKZF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,20011
Polymers143,0293
Non-polymers1,1718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.892, 180.892, 555.884
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-1304-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 69 or (resid 70 and (name...
21chain D
12(chain B and (resid 1 through 772 or (resid 773...
22(chain E and (resid 1 through 773 or (resid 774...
13chain C
23chain F
14chain L
24chain M

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 69 or (resid 70 and (name...A69
121(chain A and (resid 69 or (resid 70 and (name...A70
131(chain A and (resid 69 or (resid 70 and (name...A69 - 442
141(chain A and (resid 69 or (resid 70 and (name...A69 - 442
151(chain A and (resid 69 or (resid 70 and (name...A69 - 442
161(chain A and (resid 69 or (resid 70 and (name...A69 - 442
211chain DD69 - 442
112(chain B and (resid 1 through 772 or (resid 773...B1 - 772
122(chain B and (resid 1 through 772 or (resid 773...B773 - 776
132(chain B and (resid 1 through 772 or (resid 773...B1 - 1140
142(chain B and (resid 1 through 772 or (resid 773...B1 - 1140
152(chain B and (resid 1 through 772 or (resid 773...B1 - 1140
162(chain B and (resid 1 through 772 or (resid 773...B1 - 1140
212(chain E and (resid 1 through 773 or (resid 774...E1 - 773
222(chain E and (resid 1 through 773 or (resid 774...E774 - 776
232(chain E and (resid 1 through 773 or (resid 774...E1 - 1140
242(chain E and (resid 1 through 773 or (resid 774...E1 - 1140
252(chain E and (resid 1 through 773 or (resid 774...E1 - 1140
262(chain E and (resid 1 through 773 or (resid 774...E1 - 1140
113chain CC136 - 201
213chain FF136 - 201
114chain LL1
214chain MM1

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein Protein cereblon


Mass: 46465.375 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#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: 93347.078 Da / Num. of mol.: 2
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

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide IKZF2


Mass: 3216.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNFN1A2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53SU9

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Non-polymers , 5 types, 34 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-LWK / (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione


Mass: 417.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27N3O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.59 Å3/Da / Density % sol: 73.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M potassium/sodium phosphate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→49.89 Å / Num. obs: 93823 / % possible obs: 100 % / Redundancy: 16.4 % / Biso Wilson estimate: 88.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.062 / Rrim(I) all: 0.255 / Net I/σ(I): 11.9 / Num. measured all: 1537361
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.15-3.216.42.8117465945490.3930.7082.91.3100
17.25-49.8913.40.04593266960.9990.0120.04641.295.9

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6H0F

6h0f


Resolution: 3.15→49.89 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 4704 5.02 %
Rwork0.2127 88970 -
obs0.2142 93674 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 310.49 Å2 / Biso mean: 117.1793 Å2 / Biso min: 67.15 Å2
Refinement stepCycle: final / Resolution: 3.15→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19355 0 121 19 19495
Biso mean--123.87 90.92 -
Num. residues----2456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2274X-RAY DIFFRACTION5.192TORSIONAL
12D2274X-RAY DIFFRACTION5.192TORSIONAL
21B5006X-RAY DIFFRACTION5.192TORSIONAL
22E5006X-RAY DIFFRACTION5.192TORSIONAL
31C166X-RAY DIFFRACTION5.192TORSIONAL
32F166X-RAY DIFFRACTION5.192TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.15-3.190.43351630.378429053068
3.19-3.220.36081510.35429143065
3.22-3.260.39981770.339228873064
3.26-3.30.33291670.334528973064
3.3-3.350.36381370.326229543091
3.35-3.390.33561670.301928763043
3.39-3.440.32081630.303229053068
3.44-3.490.31331600.287729213081
3.49-3.550.30481560.277129413097
3.55-3.610.31261410.264129203061
3.61-3.670.30821430.262229273070
3.67-3.730.26411610.25129063067
3.73-3.810.29581470.242929413088
3.81-3.880.27111540.233629493103
3.88-3.970.23731670.225629213088
3.97-4.060.25271470.210329393086
4.06-4.160.26071390.200629683107
4.16-4.270.23491470.186729413088
4.27-4.40.2491380.181529863124
4.4-4.540.18961670.162429453112
4.54-4.70.15471550.159929523107
4.7-4.890.20111380.160930133151
4.89-5.120.18441690.167129453114
5.12-5.380.23721490.188529993148
5.38-5.720.23691530.195730053158
5.72-6.160.2611860.202929853171
6.16-6.780.20751680.198830223190
6.78-7.760.18971770.186330473224
7.76-9.760.18771470.161631403287
9.77-49.890.23361700.215133193489
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)
11.70610.5005-0.69462.0459-1.35282.15910.08-0.28150.04550.1218-0.0474-0.00740.0533-0.036101.1757-0.23970.04990.96370.04151.0685-35.8255-96.910677.5358
22.50541.84320.59822.1061-0.0281.6574-0.1240.53360.2041-0.22420.0181-0.0221-0.3411-0.246201.3285-0.2503-0.15090.9940.15931.2314-67.7358-96.167265.1671
31.2981-1.0127-0.70942.65880.40191.9299-0.0655-0.26130.06910.29580.2027-0.14070.13790.2218-00.9958-0.14570.09080.9162-0.09360.9334-10.8635-63.44181.951
43.44231.47811.71274.23290.64983.0091-0.01150.21430.5339-0.54490.02850.4078-0.3246-0.2061-0.00051.2594-0.13420.14520.90380.18360.7824-24.4233-61.786250.3806
53.31390.15490.96321.89110.09112.34880.0240.4028-0.5381-0.62140.17480.30520.7094-0.2087-0.00011.3714-0.24850.1650.9065-0.0140.8856-23.0705-86.20149.3102
60.6372-0.41380.91541.7084-0.35732.1444-0.24680.15170.30090.07650.2394-0.47340.4780.4219-0.00021.25450.06520.24390.9777-0.16691.18716.0132-87.405360.5358
70.22260.0401-0.04190.0653-0.03570.0357-0.21350.47260.2869-0.69360.19690.02020.1225-0.9263-0.00211.3841-0.4058-0.26791.59710.12491.1923-86.9464-108.675474.2105
80.09930.0185-0.12640.0052-0.01460.1187-0.17960.0244-0.1640.3790.50120.07260.1461-0.51490.00111.2746-0.2059-0.09530.9344-0.08650.9306-80.0674-104.717476.6767
90.0676-0.0481-0.02520.03860.03080.19920.53720.0254-0.5443-0.42330.0369-0.74230.14710.3558-0.00091.465-0.0801-0.09791.00570.09970.9139-74.2906-108.577980.5629
102.74320.5209-1.51720.86860.30742.392-0.1270.26070.036-0.15960.0717-0.01820.01880.1734-00.8757-0.02570.06941.16240.09181.014920.5201-21.38499.2197
112.88921.1021.14160.88790.48192.11140.0879-0.38250.15550.35970.01630.3675-0.379-0.3417-00.81210.01210.07261.48210.00011.177135.87211.483129.4595
121.2527-0.6642-0.10423.1802-0.64241.63230.05910.20280.0612-0.3724-0.02840.09240.1825-0.197-0.00010.8084-0.11540.00631.15980.07290.9256-20.8329-24.5583.2101
133.3450.4212-0.10292.10510.71722.0569-0.0298-0.52210.20570.5473-0.0428-0.24060.03730.1705-00.9914-0.04210.06811.09020.13650.8263-2.7926-26.928837.4826
142.9444-0.79-0.50991.46911.69613.1132-0.0758-0.062-0.81020.2819-0.14110.13161.020.2103-0.00041.3762-0.08650.21310.91610.14421.2098-7.1163-53.427319.6712
150.09790.0723-0.1150.1408-0.21830.2320.3217-0.3568-0.3904-0.0462-0.7781-0.2715-0.35670.7761-0.00130.8807-0.0201-0.14071.50160.00321.168351.767212.123121.5278
160.0361-0.0326-0.01540.0546-0.00650.0854-0.19230.3229-1.0743-0.3189-0.34990.2775-0.02770.0639-0.00290.8586-0.07590.11451.60690.16950.842949.78185.817414.5592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 317 )A69 - 317
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 442 )A318 - 442
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 336 )B1 - 336
4X-RAY DIFFRACTION4chain 'B' and (resid 337 through 810 )B337 - 810
5X-RAY DIFFRACTION5chain 'B' and (resid 811 through 1061 )B811 - 1061
6X-RAY DIFFRACTION6chain 'B' and (resid 1062 through 1140 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 136 through 140 )C136 - 140
8X-RAY DIFFRACTION8chain 'C' and (resid 141 through 151 )C141 - 151
9X-RAY DIFFRACTION9chain 'C' and (resid 152 through 163 )C152 - 163
10X-RAY DIFFRACTION10chain 'D' and (resid 69 through 317 )D69 - 317
11X-RAY DIFFRACTION11chain 'D' and (resid 318 through 442 )D318 - 442
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 336 )E1 - 336
13X-RAY DIFFRACTION13chain 'E' and (resid 337 through 991 )E337 - 991
14X-RAY DIFFRACTION14chain 'E' and (resid 992 through 1140 )E992 - 1140
15X-RAY DIFFRACTION15chain 'F' and (resid 136 through 151 )F136 - 151
16X-RAY DIFFRACTION16chain 'F' and (resid 152 through 163 )F152 - 163

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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