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- PDB-9tdz: Crystal structure of beta-TrCP bound by diphosphorylated claspin ... -

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Basic information

Entry
Database: PDB / ID: 9tdz
TitleCrystal structure of beta-TrCP bound by diphosphorylated claspin degron peptide
Components
  • Claspin
  • F-box/WD repeat-containing protein 1A
KeywordsTRANSFERASE / E3 ligase / phosphodegron / beta-TrCP / claspin
Function / homology
Function and homology information


DNA secondary structure binding / protein phosphorylated amino acid binding / regulation of cell cycle process / anaphase-promoting complex binding / positive regulation of circadian rhythm / DNA replication checkpoint signaling / mitotic DNA replication checkpoint signaling / ubiquitin ligase activator activity / regulation of canonical Wnt signaling pathway / protein dephosphorylation ...DNA secondary structure binding / protein phosphorylated amino acid binding / regulation of cell cycle process / anaphase-promoting complex binding / positive regulation of circadian rhythm / DNA replication checkpoint signaling / mitotic DNA replication checkpoint signaling / ubiquitin ligase activator activity / regulation of canonical Wnt signaling pathway / protein dephosphorylation / non-canonical NF-kappaB signal transduction / Apoptotic cleavage of cellular proteins / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / mitotic G2 DNA damage checkpoint signaling / ligase activity / Prolactin receptor signaling / positive regulation of proteolysis / negative regulation of T cell receptor signaling pathway / Activation of ATR in response to replication stress / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / DNA damage checkpoint signaling / negative regulation of smoothened signaling pathway / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / 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 / Neddylation / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein dimerization activity / Ub-specific processing proteases / protein ubiquitination / DNA repair / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / Claspin / 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 / : / Claspin / 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 / 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
Claspin / F-box/WD repeat-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.346 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 24, 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: Claspin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,72511
Polymers43,2042
Non-polymers5219
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint15 kcal/mol
Surface area15290 Å2
Unit cell
Length a, b, c (Å)44.498, 46.859, 150.141
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 Claspin / hClaspin


Mass: 1374.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLSPN / Production host: synthetic construct (others) / References: UniProt: Q9HAW4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 32.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG4K, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.346→75.071 Å / Num. obs: 49954 / % possible obs: 92.2 % / Redundancy: 6.8 % / CC1/2: 0.996 / Net I/σ(I): 6.7
Reflection shellResolution: 1.346→1.495 Å / Num. unique obs: 2498 / CC1/2: 0.462

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.346→25.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 2602 -RANDOM
Rwork0.1775 ---
obs0.179 49941 70.8 %-
Displacement parametersBiso mean: 21.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.3288 Å20 Å20 Å2
2--0.0646 Å20 Å2
3----0.3935 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.346→25.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 33 285 3259
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123036HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.174097HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1080SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes515HARMONIC5
X-RAY DIFFRACTIONt_it3036HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion391SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3065SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.15
X-RAY DIFFRACTIONt_other_torsion13.81
LS refinement shellResolution: 1.35→1.46 Å
RfactorNum. reflection% reflection
Rfree0.2668 42 -
Rwork0.2661 --
obs0.2661 999 6.47 %

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