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- PDB-9nfr: Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1 -

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Basic information

Entry
Database: PDB / ID: 9nfr
TitleCrystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1
Components
  • DNA damage-binding protein 1
  • Protein cereblon
  • Proto-oncogene vav
KeywordsLIGASE / Ternary complex / Molecular glue degrader / E3 ligase / neosubstrate
Function / homology
Function and homology information


immune response-regulating cell surface receptor signaling pathway / negative regulation of monoatomic ion transmembrane transport / phosphorylation-dependent protein binding / positive regulation of natural killer cell mediated cytotoxicity / 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 / natural killer cell activation ...immune response-regulating cell surface receptor signaling pathway / negative regulation of monoatomic ion transmembrane transport / phosphorylation-dependent protein binding / positive regulation of natural killer cell mediated cytotoxicity / 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 / natural killer cell activation / regulation of small GTPase mediated signal transduction / Azathioprine ADME / CD28 dependent Vav1 pathway / biological process involved in interaction with symbiont / regulation of GTPase activity / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / natural killer cell mediated cytotoxicity / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / regulation of cell size / negative regulation of reproductive process / negative regulation of developmental process / Fc-epsilon receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / locomotory exploration behavior / cullin family protein binding / viral release from host cell / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / RHOG GTPase cycle / positive regulation of Wnt signaling pathway / RHOA GTPase cycle / RAC2 GTPase cycle / ectopic germ cell programmed cell death / vascular endothelial growth factor receptor signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / Erythropoietin activates RAS / GPVI-mediated activation cascade / T cell costimulation / RAC1 GTPase cycle / neutrophil chemotaxis / phosphotyrosine residue binding / positive regulation of gluconeogenesis / FCERI mediated Ca+2 mobilization / reactive oxygen species metabolic process / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / guanyl-nucleotide exchange factor activity / VEGFR2 mediated vascular permeability / integrin-mediated signaling pathway / nucleotide-excision repair / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of signaling by CBL / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / Signaling by SCF-KIT / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Regulation of actin dynamics for phagocytic cup formation / platelet activation / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / VEGFA-VEGFR2 Pathway / Wnt signaling pathway / 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 / Constitutive Signaling by Aberrant PI3K in Cancer / cellular response to UV / rhythmic process / cellular response to xenobiotic stimulus / cell-cell junction / cell migration / G alpha (12/13) signalling events / PIP3 activates AKT signaling / site of double-strand break / Neddylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / G protein-coupled receptor signaling pathway / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding
Similarity search - Function
VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Guanine-nucleotide dissociation stimulator, CDC24, conserved site ...VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / 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) / Calponin homology 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 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. / PUA-like superfamily / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / Proto-oncogene vav / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsTrenh, P. / Bunker, R.D. / Lucas, X. / Gainza, P. / Tsai, J.H.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mining the CRBN Target Space Redefines Rules for Molecular Glue-induced Neosubstrate Recognition
Authors: Petzold, G. / Gainza, P. / Annunziato, S. / Lamberto, I. / Trenh, P. / McAllister, L.A. / DeMarco, B. / Schwander, L. / Bunker, R.D. / Zlotosch, M. / SriRamaratnam, R. / Gilberto, S. / ...Authors: Petzold, G. / Gainza, P. / Annunziato, S. / Lamberto, I. / Trenh, P. / McAllister, L.A. / DeMarco, B. / Schwander, L. / Bunker, R.D. / Zlotosch, M. / SriRamaratnam, R. / Gilberto, S. / Langousis, G. / Donckele, E.J. / Quan, C. / Strande, V. / De Donatis, G.M. / Alabi, S.B. / Alers, J. / Matysik, M. / Staehly, C. / Dubois, A. / Osmont, A. / Garskovas, M. / Lyon, D. / Wiedmer, L. / Oleinikovas, V. / Lieberherr, R. / Rubin, N.T. / Lam, D.T. / Ilic-Widlund, N. / Ritzen, A. / Caceres, R.M. / Vigil, D. / Tsai, J.H.C. / Wallace, O. / Peluso, M. / Sadok, A. / Paterson, A.M. / Zarayskiy, V. / Fasching, B. / Bonenfant, D. / Warmuth, M. / Castle, J. / Townson, S.A.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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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
C: Proto-oncogene vav
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,0905
Polymers184,6153
Non-polymers4752
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-34 kcal/mol
Surface area63820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.599, 143.599, 367.636
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)

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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: 50603.676 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#3: Protein Proto-oncogene vav


Mass: 6913.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV1, VAV / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P15498
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-A1BYX / (3R)-3-{2-chloro-4'-[(1-methyl-1H-pyrazol-3-yl)methoxy][1,1'-biphenyl]-3-yl}piperidine-2,6-dione


Mass: 409.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.6 % PEG Smear Low, 6.1 % PEG Smear Medium, 4.3 % PEG Smear High, 5 % glycerol, 0.1 M CaCl2, and 0.1 M MES pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95375 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 3.4→56.58 Å / Num. obs: 31052 / % possible obs: 98.2 % / Redundancy: 38.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.336 / Net I/σ(I): 12.3
Reflection shellResolution: 3.4→3.51 Å / Num. unique obs: 2011 / CC1/2: 0.404

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Processing

Software
NameVersionClassification
PHENIXdev_5430refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→55.45 Å / SU ML: 0.4365 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2315
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2708 1528 4.92 %
Rwork0.2108 29523 -
obs0.2136 31051 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 129.48 Å2
Refinement stepCycle: LAST / Resolution: 3.4→55.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12071 0 22 0 12093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112332
X-RAY DIFFRACTIONf_angle_d1.329516704
X-RAY DIFFRACTIONf_chiral_restr0.09071892
X-RAY DIFFRACTIONf_plane_restr0.00532164
X-RAY DIFFRACTIONf_dihedral_angle_d16.32214598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.510.32861100.29462010X-RAY DIFFRACTION75.23
3.51-3.640.3291210.282683X-RAY DIFFRACTION99.89
3.64-3.780.31381440.26812706X-RAY DIFFRACTION100
3.78-3.950.31761500.25132660X-RAY DIFFRACTION99.93
3.95-4.160.30131340.21892703X-RAY DIFFRACTION100
4.16-4.420.25521380.20712705X-RAY DIFFRACTION99.96
4.42-4.760.2381390.17532743X-RAY DIFFRACTION100
4.76-5.240.26461510.17312727X-RAY DIFFRACTION100
5.24-60.2931610.20862760X-RAY DIFFRACTION100
6-7.550.27511420.22262813X-RAY DIFFRACTION99.97
7.56-55.450.23141380.19453013X-RAY DIFFRACTION99.72
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)
10.696756752493980.085220038076129-0.259111768962120.41070541423555-0.460679835473350.478512627857480.103181351809310.136038951570380.30380599943551-0.666787005023050.0283575018876030.0612967671522490.10698518664042-0.113558824529490.0801887456801731.3161521201937-0.17429990279896-0.180168147934060.672921148914360.172884230672360.42882045175278-8.742669094842570.230627044739-19.263393956016
21.0450354627001-0.291056333263780.00266686703881921.14802379456280.295873732157890.905697888201290.0817758882277490.0986409506599170.084258302021751-0.353752998541250.0961755435734350.0997741475805990.076010530073915-0.248183957714280.137922189446190.61654549688759-0.18344993401428-0.108126777957050.517892088293490.167159978620180.60927067734204-15.57642300274878.50935336395114.121270807209
30.198770018810980.28501846858017-0.0357899799769630.089637524654736-0.0133688689273380.34102478314685-0.084132970819478-0.40457448300328-0.16137679110270.014306106457489-0.511700617242170.2494147154961-0.22889811061085-0.21484421523514-0.031871718780670.81756552295654-0.10140189834912-0.149453775886950.52002663934856-0.183637856882390.77477940996953-46.0238329376630.075199656639-15.55352797416
4-0.001469403294587-0.000369247985428150.0173262834486550.00287517302481370.0187590310290760.040497387016041-0.085809548525530.0279855712600060.0795436168964920.12178952971175-0.35838201907247-0.120602321737010.336750805843120.361563156742496.5534571151448E-71.6041872572092-0.18155959197045-0.451716752616041.1479960045812-0.0632923547371060.98914723668997-10.34472356226853.584334945558-13.507531707171
50.020836747826461-0.003002599772314-0.0171921871904680.011834252740705-0.00694957734225780.0140902526143750.0731911971564420.119660975135890.0230766801960010.168528896742780.00860379413606510.45708889710124-0.246249041406120.024990865464107-1.1021680998607E-71.214496036372-0.21963696134816-0.186543298203520.8011110480891-0.0748007146777120.91756350339272-8.934549143091647.445877095117-4.7660161475702
60.35422363967702-0.42751363055023-0.082169438854050.361475266982880.0582355756301440.43083678393196-0.41179049695826-0.0988983657182860.15314054979741-0.375828388102140.474344084855380.343896738685350.337032127281870.288856534475960.0270893714223221.1649580040684-0.24520286557342-0.181949009653170.52759806275020.112762166655850.72484970040625-25.51587830477320.491090114132-8.1559673454867
70.0024921762510112-0.00541926335301690.0053982977265908-0.00430970622353120.00356587434793480.011716316975359-0.064976020589147-0.045161689681234-0.0839750142691480.022141391104262-0.1825904918604-0.10988716166348-0.47981697443841-0.234829693098452.795461304463E-62.1124117086646-0.29861517908852-0.46799462354911.66688886215120.178044521077481.7533642648316-50.868969522614-4.0762207298959-9.0957498649025
80.00182937755675450.00125370981722-0.0047284769835640.011761541448116-0.0237006777808040.015802724138849-0.105210186896980.44425754627892-0.011195719469164-0.089729771730315-0.29584854866599-0.13268124072959-0.33265864675379-0.20093796618792-6.8961460981008E-71.5198124550727-0.31909194140193-0.160533741508820.973442983388360.246235321664451.5798321904095-48.6036669469733.6670553295579-7.8974303314746
90.00435111641240250.0074133429104780.00183303069115250.00850436624687010.00303191184788530.00089901030012226-0.0954570340726650.00061645850682299-0.0725028246876220.081866412780685-0.16353851240112-0.15821340287048-0.05071648276645-0.045731002603277-8.7694961016255E-62.32517282285560.090231476443208-0.404249403649071.6687993249456-0.059072519524691.8725071174167-49.6873187739364.5152760093461-20.279683516263
10-0.0018578175993407-0.00183760609991060.000111325855614380.00547494525538890.0020069857950704-0.000737623123642490.23770001967942-0.227011933820810.0396603218318460.2798538460464-0.0492032647814870.17752686304826-0.016907960417111-0.030547565989855-3.9187034154335E-61.7266813721266-0.10896564737707-0.170569447991191.71124062799880.19425536780092.6526986998992-52.4215682551227.6979347655628-6.7698654098495
110.00886238675793220.00731063956023770.00581846886930210.00966161523688250.00904281614089640.00709835979792190.0628107553556320.051534636410536-0.199922867855630.0274308358780240.00118027839276190.0540932082030950.020393192713710.048715374209683-2.6330466574073E-71.7321359220557-0.1728997878965-0.384747439942892.12845937228950.383346467460922.6063454860094-50.4601295324740.39389744167172-13.649169895222
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 365 )AA2 - 3651 - 364
22chain 'A' and (resid 366 through 1140 )AA366 - 1140365 - 1119
33chain 'B' and (resid 77 through 194 )BB77 - 1941 - 118
44chain 'B' and (resid 195 through 219 )BB195 - 219119 - 136
55chain 'B' and (resid 220 through 249 )BB220 - 249137 - 166
66chain 'B' and (resid 250 through 436 )BB250 - 436167 - 353
77chain 'C' and (resid 785 through 794 )CE785 - 7941 - 10
88chain 'C' and (resid 795 through 813 )CE795 - 81311 - 29
99chain 'C' and (resid 814 through 820 )CE814 - 82030 - 36
1010chain 'C' and (resid 821 through 828 )CE821 - 82837 - 44
1111chain 'C' and (resid 829 through 839 )CE829 - 83945 - 55

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