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- PDB-5hxb: Cereblon in complex with DDB1, CC-885, and GSPT1 -

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Basic information

Entry
Database: PDB / ID: 5hxb
TitleCereblon in complex with DDB1, CC-885, and GSPT1
Components
  • DNA damage-binding protein 1
  • Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
  • Protein cereblon
KeywordsLIGASE / E3 / ubiquitin / DCAF / cereblon / DDB1 / CRL4 / cullin / IMiD / GSPT1 / CRBN
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 / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair ...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 / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / 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 / 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 / positive regulation of Wnt signaling pathway / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / translational termination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / 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 / Wnt signaling pathway / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / translation / DNA repair / GTPase activity / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / GTP binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / 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 / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / : / GTP-eEF1A C-terminal domain-like ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Peptide methionine sulfoxide reductase. / DNA polymerase; domain 1 - #910 / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / : / GTP-eEF1A C-terminal domain-like / : / 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) / Elongation factor Tu C-terminal domain / 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 / Translation factors / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Beta Complex / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / Translation protein, beta-barrel domain superfamily / Roll / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-85C / 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: 3.6 Å
AuthorsChamberlain, P.P. / Matyskiela, M. / Pagarigan, B.
CitationJournal: Nature / Year: 2016
Title: A novel cereblon modulator recruits GSPT1 to the CRL4(CRBN) ubiquitin ligase.
Authors: Matyskiela, M.E. / Lu, G. / Ito, T. / Pagarigan, B. / Lu, C.C. / Miller, K. / Fang, W. / Wang, N.Y. / Nguyen, D. / Houston, J. / Carmel, G. / Tran, T. / Riley, M. / Nosaka, L. / Lander, G.C. ...Authors: Matyskiela, M.E. / Lu, G. / Ito, T. / Pagarigan, B. / Lu, C.C. / Miller, K. / Fang, W. / Wang, N.Y. / Nguyen, D. / Houston, J. / Carmel, G. / Tran, T. / Riley, M. / Nosaka, L. / Lander, G.C. / Gaidarova, S. / Xu, S. / Ruchelman, A.L. / Handa, H. / Carmichael, J. / Daniel, T.O. / Cathers, B.E. / Lopez-Girona, A. / Chamberlain, P.P.
History
DepositionJan 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence ...citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)392,39210
Polymers391,3806
Non-polymers1,0134
Water00
1
X: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
Y: DNA damage-binding protein 1
Z: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1965
Polymers195,6903
Non-polymers5062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA damage-binding protein 1
C: Protein cereblon
A: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1965
Polymers195,6903
Non-polymers5062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.747, 111.522, 175.057
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21A
12Y
22B
13Z
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEVALVALXA440 - 6335 - 198
21ILEILEVALVALAF440 - 6335 - 198
12SERSERHISHISYB2 - 11402 - 1140
22SERSERHISHISBD2 - 11402 - 1140
13ASNASNLEULEUZC48 - 44212 - 406
23ASNASNLEULEUCE48 - 44212 - 406

NCS ensembles :
ID
1
2
3
Detailstrimeric as determined by electron microscopy

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Components

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


Mass: 21995.799 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
#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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#3: Protein Protein cereblon


Mass: 46596.566 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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-85C / 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea


Mass: 440.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21ClN4O4
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: 3.89 Å3/Da / Density % sol: 68.37 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / Details: 200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350 / PH range: 8.4 - 8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 66582 / % possible obs: 94.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 10.6
Reflection shellResolution: 3.6→3.66 Å / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3343 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZ4, 3E1Y

4tz4

3e1y


Resolution: 3.6→50 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.858 / SU B: 64.833 / SU ML: 0.536 / Cross valid method: THROUGHOUT / ESU R Free: 0.644 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3289 5 %RANDOM
Rwork0.224 ---
obs0.226 62827 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 112.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å20 Å21.25 Å2
2---8.14 Å20 Å2
3---5.16 Å2
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25025 0 64 0 25089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01925592
X-RAY DIFFRACTIONr_bond_other_d0.0040.0224215
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.96334776
X-RAY DIFFRACTIONr_angle_other_deg1.0122.99955467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.8853250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.51624.5511035
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.831154184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3815115
X-RAY DIFFRACTIONr_chiral_restr0.1460.24102
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02128846
X-RAY DIFFRACTIONr_gen_planes_other0.0080.025609
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_it9.5146.52513138
X-RAY DIFFRACTIONr_mcbond_other9.5126.52513137
X-RAY DIFFRACTIONr_mcangle_it14.6349.78316342
X-RAY DIFFRACTIONr_mcangle_other14.6349.78316343
X-RAY DIFFRACTIONr_scbond_it9.2177.04212454
X-RAY DIFFRACTIONr_scbond_other9.2147.04212453
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.42910.31618435
X-RAY DIFFRACTIONr_long_range_B_refined22.27758.11551500
X-RAY DIFFRACTIONr_long_range_B_other22.27758.11651501
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11X225920.11
12A225920.11
21Y1293400.05
22B1293400.05
31Z425440.07
32C425440.07
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 233 -
Rwork0.388 4579 -
obs--93.87 %
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)
10.1669-0.5212-0.00271.74760.30250.8982-0.10670.0006-0.07020.32570.09180.17790.27990.06940.01490.93630.0250.04620.6926-0.08440.41449.4674-80.7292102.4795
20.41580.79720.07122.56711.14721.024-0.0522-0.03010.1022-0.45490.09150.1168-0.31320.0059-0.03941.0017-0.03230.08530.686-0.08440.425412.1104-4.775475.5159
30.73320.3015-0.50041.4065-0.29640.91590.0538-0.29710.07740.32520.0718-0.69340.26320.4855-0.12560.59110.2377-0.18521.061-0.26280.655542.819-37.9069134.6649
40.8227-0.02230.17230.9281-0.41641.2015-0.00830.1339-0.0372-0.1003-0.0077-0.4126-0.16420.45440.0160.532-0.19140.17411.0248-0.22070.581751.36-47.044150.1205
50.41530.0113-0.51531.1105-0.18510.0036-0.0950.1153-0.0870.1229-0.0882-0.01320.0048-0.12650.77390.06920.03220.7601-0.06850.277710.5444-31.3976116.7175
60.33180.08650.09541.0848-0.05620.828-0.01320.0725-0.04120.03770.1559-0.049-0.01250.0552-0.14270.7733-0.04840.06110.7512-0.07080.263416.0754-54.121261.7448
71.335-0.0519-0.41741.04051.46873.5667-0.1643-0.059-0.25810.21150.2056-0.0976-0.11210.1831-0.04130.79940.1250.01490.6645-0.02810.35623.8159-2.7506155.7365
82.1656-0.92510.98991.76040.90133.1635-0.07230.00230.15580.00720.194-0.08720.13810.0282-0.12170.8382-0.15060.06090.6778-0.04480.296517.5574-82.477322.236
91.1325-0.92120.39582.79620.31880.3688-0.0722-0.02440.024-0.60110.2751-0.3557-0.24250.0484-0.20291.213-0.06630.21160.7682-0.05780.32183.942512.9862134.8985
101.7020.37250.10392.01081.17950.72120.00620.07890.01550.55740.2343-0.27020.30330.1099-0.24051.24290.04-0.06650.7348-0.02570.245513.4798-98.152543.1082
112.2282-0.82810.94135.2409-0.55642.9811-0.1887-0.09650.21310.195-0.0543-0.50380.03640.43530.2430.8919-0.18770.15310.866-0.09730.432312.709337.9356176.0349
123.32440.1333-0.39763.0612-0.82941.7296-0.0344-0.2382-0.0997-0.3857-0.0149-0.00730.55160.58070.04930.91480.1711-0.01910.8093-0.04390.323329.8786-123.57134.2636
130.67650.43210.35560.61710.53350.5130.10930.07420.0410.1363-0.0418-0.0405-0.0102-0.1301-0.06750.5270.03850.0960.39650.02650.0363-7.466327.9491158.6586
140.7963-0.6633-0.6980.68231.08562.7649-0.0679-0.1655-0.01140.05770.1342-0.05580.2306-0.1212-0.06631.0171-0.0863-0.01550.7851-0.01060.33187.1093-113.388317.5169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B394 - 672
2X-RAY DIFFRACTION2Y394 - 672
3X-RAY DIFFRACTION3B11 - 355
4X-RAY DIFFRACTION4Y11 - 355
5X-RAY DIFFRACTION5B713 - 1081
6X-RAY DIFFRACTION6Y713 - 1081
7X-RAY DIFFRACTION7C60 - 186
8X-RAY DIFFRACTION8Z60 - 186
9X-RAY DIFFRACTION9C319 - 442
10X-RAY DIFFRACTION10Z319 - 442
11X-RAY DIFFRACTION11A437 - 523
12X-RAY DIFFRACTION12X437 - 523
13X-RAY DIFFRACTION13A526 - 634
14X-RAY DIFFRACTION14X526 - 634

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