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- PDB-9t9w: Crystal structure of beta-TrCP bound by diphosphorylated I-kappa-... -

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Basic information

Entry
Database: PDB / ID: 9t9w
TitleCrystal structure of beta-TrCP bound by diphosphorylated I-kappa-B-alpha degron peptide
Components
  • F-box/WD repeat-containing protein 1A
  • NF-kappa-B inhibitor alpha
KeywordsTRANSFERASE / E3 ligase / phosphodegron / beta-TrCP / i-kappa-B-alpha
Function / homology
Function and homology information


negative regulation of cholesterol transport / : / I-kappaB/NF-kappaB complex / protein phosphorylated amino acid binding / nucleotide-binding oligomerization domain containing 1 signaling pathway / negative regulation of myeloid cell differentiation / IkBA variant leads to EDA-ID / regulation of cell cycle process / positive regulation of circadian rhythm / nucleotide-binding oligomerization domain containing 2 signaling pathway ...negative regulation of cholesterol transport / : / I-kappaB/NF-kappaB complex / protein phosphorylated amino acid binding / nucleotide-binding oligomerization domain containing 1 signaling pathway / negative regulation of myeloid cell differentiation / IkBA variant leads to EDA-ID / regulation of cell cycle process / positive regulation of circadian rhythm / nucleotide-binding oligomerization domain containing 2 signaling pathway / SUMOylation of immune response proteins / RIP-mediated NFkB activation via ZBP1 / ubiquitin ligase activator activity / interleukin-1-mediated signaling pathway / regulation of canonical Wnt signaling pathway / toll-like receptor 4 signaling pathway / nuclear localization sequence binding / protein dephosphorylation / negative regulation of protein import into nucleus / non-canonical NF-kappaB signal transduction / cellular response to cold / response to muramyl dipeptide / response to exogenous dsRNA / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ligase activity / Prolactin receptor signaling / positive regulation of proteolysis / TRAF6 mediated NF-kB activation / negative regulation of Notch signaling pathway / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / positive regulation of transcription initiation by RNA polymerase II / Notch signaling pathway / negative regulation of T cell receptor signaling pathway / molecular sequestering activity / NF-kappaB binding / response to muscle stretch / transcription regulator inhibitor activity / canonical NF-kappaB signal transduction / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / ubiquitin-like ligase-substrate adaptor activity / lipopolysaccharide-mediated signaling pathway / protein K48-linked ubiquitination / negative regulation of cytokine production involved in inflammatory response / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / NF-kB is activated and signals survival / B cell receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / negative regulation of smoothened signaling pathway / MAP3K8 (TPL2)-dependent MAPK1/3 activation / protein sequestering activity / Deactivation of the beta-catenin transactivating complex / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / protein import into nucleus / Vpu mediated degradation of CD4 / protein destabilization / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / regulation of circadian rhythm / beta-catenin binding / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / positive regulation of inflammatory response / protein polyubiquitination / Interleukin-1 signaling / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Regulation of PLK1 Activity at G2/M Transition / regulation of cell population proliferation / rhythmic process / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein dimerization activity / Ub-specific processing proteases / protein ubiquitination / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain ...: / D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
NF-kappa-B inhibitor alpha / F-box/WD repeat-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.162 Å
AuthorsCollie, G.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2026
Title: Structural Studies of beta TrCP Reveal Plasticity in Binding Modes of Consensus and Nonconsensus Degrons.
Authors: Collie, G.W. / Mak, H. / Acebron-Garcia-de-Eulate, M. / Argyrou, A. / Couturier, M. / Cuomo, M.E. / O Donovan, D.H. / Russell, I.C. / Wells, G. / Winter-Holt, J.
History
DepositionNov 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 27, 2026Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F-box/WD repeat-containing protein 1A
C: NF-kappa-B inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7418
Polymers43,3682
Non-polymers3726
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint6 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.602, 46.822, 150.381
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein F-box/WD repeat-containing protein 1A / E3RSIkappaB / Epididymis tissue protein Li 2a / F-box and WD repeats protein beta-TrCP / ...E3RSIkappaB / Epididymis tissue protein Li 2a / F-box and WD repeats protein beta-TrCP / pIkappaBalpha-E3 receptor subunit


Mass: 41829.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTRC, BTRCP, FBW1A, FBXW1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y297
#2: Protein/peptide NF-kappa-B inhibitor alpha / I-kappa-B-alpha / IkB-alpha / IkappaBalpha / Major histocompatibility complex enhancer-binding protein MAD3


Mass: 1538.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKBIA, IKBA, MAD3, NFKBI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25963
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.81 Å3/Da / Density % sol: 32.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18% PEG8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.162→44.705 Å / Num. obs: 86137 / % possible obs: 94.3 % / Redundancy: 6.2 % / CC1/2: 0.992 / Net I/σ(I): 6.9
Reflection shellResolution: 1.162→1.277 Å / Num. unique obs: 4307 / CC1/2: 0.412

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.162→23.13 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.051 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.053 / SU Rfree Blow DPI: 0.054 / SU Rfree Cruickshank DPI: 0.052
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 4283 -RANDOM
Rwork0.1899 ---
obs0.1911 86121 78.8 %-
Displacement parametersBiso mean: 16.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.024 Å20 Å20 Å2
2--0.0576 Å20 Å2
3----0.0335 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.162→23.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 24 338 3302
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0143049HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.284119HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1096SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes519HARMONIC5
X-RAY DIFFRACTIONt_it3049HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion396SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3217SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.76
X-RAY DIFFRACTIONt_other_torsion14.29
LS refinement shellResolution: 1.162→1.25 Å
RfactorNum. reflection% reflection
Rfree0.2633 83 -
Rwork0.2773 --
obs--8.1 %

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