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- PDB-9fjx: Crystal structure of human CRBN-DDB1 in complex with Lenalidomide -

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Basic information

Entry
Database: PDB / ID: 9fjx
TitleCrystal structure of human CRBN-DDB1 in complex with Lenalidomide
Components
  • DNA damage-binding protein 1
  • Protein cereblon
KeywordsPROTEIN BINDING / E3-ligase / Degradation / Glue / Protac
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 / 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 / Wnt signaling pathway / Formation of Incision Complex in GG-NER / positive regulation of protein catabolic process / Dual incision in TC-NER / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
S-Lenalidomide / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLe Bihan, Y.-V. / van Montfort, R.L.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC309/A11566 United Kingdom
CitationJournal: Blood / Year: 2025
Title: Evaluating the impact of CRBN mutations on response to immunomodulatory drugs and novel cereblon E3 ligase modulators in myeloma.
Authors: Chrisochoidou, Y. / Scarpino, A. / Morales, S. / Martin, S. / Bird, S. / Li, Y. / Walker, B. / Caldwell, J. / Le Bihan, Y.V. / Pawlyn, C.
History
DepositionMay 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,77713
Polymers174,8842
Non-polymers89211
Water21,7261206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-13 kcal/mol
Surface area59570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.673, 129.068, 198.446
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#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: 128139.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein Protein cereblon


Mass: 46744.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2

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Non-polymers , 6 types, 1217 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-LVY / S-Lenalidomide


Mass: 259.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N3O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1206 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl ...Details: 0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2→49.61 Å / Num. obs: 124900 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 38.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.046 / Rrim(I) all: 0.123 / Net I/σ(I): 9.7 / Num. measured all: 900114 / Scaling rejects: 618
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
2-2.036.32.1233871961210.3090.9282.3240.999.9
10.95-49.617.10.03263048900.9990.0130.03438.499.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20.15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.175 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 6089 4.91 %RANDOM
Rwork0.196 ---
obs0.1978 124077 99.4 %-
Displacement parametersBiso max: 137.88 Å2 / Biso mean: 48.36 Å2 / Biso min: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1-3.5038 Å20 Å20 Å2
2---3.4497 Å20 Å2
3----0.0542 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2→20.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11190 0 53 1226 12469
Biso mean--52.22 53.76 -
Num. residues----1482
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3982SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2016HARMONIC5
X-RAY DIFFRACTIONt_it11774HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1590SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies55HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10506SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11774HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16014HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion15.92
LS refinement shellResolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3258 100 4.03 %
Rwork0.3125 2382 -
all0.313 2482 -
obs--98.59 %
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)
10.43440.1130.05390.5437-0.22630.6636-0.01390.03960.0158-0.0796-0.00070.0539-0.09510.02490.0146-0.00260.0048-0.0154-0.0219-0.0322-0.0258-22.7413-3.390534.0321
22.85771.3232-0.40533.92390.5353.45520.1168-0.0572-0.39170.4806-0.25460.14070.6584-0.56370.13780.0219-0.17460.05420.1137-0.0509-0.0996-35.4126-14.552991.0443
30.915-0.36020.19070.41520.00720.3744-0.0164-0.0267-0.10330.03530.05510.02570.05260.0233-0.0388-0.0501-0.0076-0.0036-0.0273-0.02060.0026-14.1621-29.521451.9271
40.4998-0.4921-0.61831.34241.2251.9529-0.04740.1494-0.05180.0563-0.29320.22480.1808-0.32420.3407-0.0115-0.00970.040.0126-0.0993-0.0589-9.9158-47.63619.6003
50.6266-1.2839-0.82011.8851.31040.82520.10620.03030.1627-0.2182-0.0175-0.1781-0.05610.0553-0.08860.0190.01470.04120.0318-0.045-0.02150.2315-30.068227.6429
61.8243-1.1403-0.34911.00660.59271.15280.0291-0.07480.1652-0.0262-0.0296-0.0813-0.01090.06780.0005-0.0140.00560.04380.0199-0.0175-0.071413.2219-48.578111.5703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - 393 }A2 - 393
2X-RAY DIFFRACTION2{ A|394 - 708 }A394 - 708
3X-RAY DIFFRACTION3{ A|709 - 1148 }A709 - 1848
4X-RAY DIFFRACTION4{ B|45 - 199 }B45 - 199
5X-RAY DIFFRACTION5{ B|200 - 329 }B200 - 329
6X-RAY DIFFRACTION6{ B|330 - 442 }B330 - 442

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