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- PDB-9tg7: Crystal structure of beta-TrCP bound by monophosphorylated WEE1 d... -

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Basic information

Entry
Database: PDB / ID: 9tg7
TitleCrystal structure of beta-TrCP bound by monophosphorylated WEE1 degron peptide
Components
  • F-box/WD repeat-containing protein 1A
  • Wee1-like protein kinase
KeywordsTRANSFERASE / E3 ligase / phosphodegron / beta-TrCP / WEE1
Function / homology
Function and homology information


protein phosphorylated amino acid binding / regulation of cell cycle process / negative regulation of G2/M transition of mitotic cell cycle / G2/M DNA replication checkpoint / positive regulation of circadian rhythm / Polo-like kinase mediated events / ubiquitin ligase activator activity / regulation of canonical Wnt signaling pathway / protein dephosphorylation / negative regulation of G1/S transition of mitotic cell cycle ...protein phosphorylated amino acid binding / regulation of cell cycle process / negative regulation of G2/M transition of mitotic cell cycle / G2/M DNA replication checkpoint / positive regulation of circadian rhythm / Polo-like kinase mediated events / ubiquitin ligase activator activity / regulation of canonical Wnt signaling pathway / protein dephosphorylation / negative regulation of G1/S transition of mitotic cell cycle / non-canonical NF-kappaB signal transduction / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ligase activity / Prolactin receptor signaling / positive regulation of proteolysis / negative regulation of T cell receptor signaling pathway / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / positive regulation of DNA replication / negative regulation of smoothened signaling pathway / MAP3K8 (TPL2)-dependent MAPK1/3 activation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Deactivation of the beta-catenin transactivating complex / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / 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 / 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 / G2/M transition of mitotic cell cycle / Degradation of beta-catenin by the destruction complex / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / Interleukin-1 signaling / ubiquitin protein ligase activity / Regulation of PLK1 Activity at G2/M Transition / rhythmic process / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / Factors involved in megakaryocyte development and platelet production / Neddylation / protein tyrosine kinase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein dimerization activity / protein ubiquitination / cell division / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / Wee1-like protein kinase / : / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily ...D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / Wee1-like protein kinase / : / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain / WD domain, G-beta repeat / G-protein beta WD-40 repeat / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Protein kinase domain / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Serine/Threonine protein kinases, catalytic domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Wee1-like protein kinase / F-box/WD repeat-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.684 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 28, 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
B: Wee1-like protein kinase


Theoretical massNumber of molelcules
Total (without water)43,1922
Polymers43,1922
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-6 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.894, 47.307, 148.272
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 / Mutation: L188E, L192E
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 Wee1-like protein kinase / WEE1hu / Wee1A kinase


Mass: 1362.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WEE1 / Production host: synthetic construct (others)
References: UniProt: P30291, non-specific protein-tyrosine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.86 Å3/Da / Density % sol: 33.99 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 20% PEG10K, 0.1 M Na-Hepes pH 7.5

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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: 1.684→74.136 Å / Num. obs: 21819 / % possible obs: 90.1 % / Redundancy: 6.9 % / CC1/2: 0.979 / Net I/σ(I): 5.1
Reflection shellResolution: 1.684→1.991 Å / Num. unique obs: 1091 / CC1/2: 0.157

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.684→74.14 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.24 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.257 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.191
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1033 -RANDOM
Rwork0.2077 ---
obs0.2099 21795 58.1 %-
Displacement parametersBiso mean: 27.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.4417 Å20 Å20 Å2
2--0.8406 Å20 Å2
3----2.2823 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.684→74.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 0 194 3095
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012958HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14003HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1049SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes501HARMONIC5
X-RAY DIFFRACTIONt_it2958HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion386SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2656SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.16
X-RAY DIFFRACTIONt_other_torsion15.86
LS refinement shellResolution: 1.684→1.91 Å
RfactorNum. reflection% reflection
Rfree0.3729 25 -
Rwork0.2882 --
obs--3.68 %

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