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- PDB-9tfu: Crystal structure of beta-TrCP bound by monophosphorylated ATF4 d... -

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Basic information

Entry
Database: PDB / ID: 9tfu
TitleCrystal structure of beta-TrCP bound by monophosphorylated ATF4 degron peptide
Components
  • Cyclic AMP-dependent transcription factor ATF-4
  • F-box/WD repeat-containing protein 1A
KeywordsTRANSFERASE / E3 ligase / phosphodegron / beta-TrCP / ATF4
Function / homology
Function and homology information


: / ATF1-ATF4 transcription factor complex / CHOP-ATF4 complex / Lewy body core / ATF4-CREB1 transcription factor complex / cAMP response element binding / leucine zipper domain binding / integrated stress response signaling / cAMP response element binding protein binding / protein phosphorylated amino acid binding ...: / ATF1-ATF4 transcription factor complex / CHOP-ATF4 complex / Lewy body core / ATF4-CREB1 transcription factor complex / cAMP response element binding / leucine zipper domain binding / integrated stress response signaling / cAMP response element binding protein binding / protein phosphorylated amino acid binding / ATF6 (ATF6-alpha) activates chaperone genes / response to manganese-induced endoplasmic reticulum stress / HRI-mediated signaling / Response of EIF2AK1 (HRI) to heme deficiency / lens fiber cell morphogenesis / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / PERK regulates gene expression / ATF4 activates genes in response to endoplasmic reticulum stress / cellular response to leucine starvation / regulation of cell cycle process / positive regulation of circadian rhythm / NFE2L2 regulating ER-stress associated genes / embryonic hemopoiesis / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / ubiquitin ligase activator activity / negative regulation of cold-induced thermogenesis / regulation of canonical Wnt signaling pathway / NFE2L2 regulating anti-oxidant/detoxification enzymes / protein dephosphorylation / non-canonical NF-kappaB signal transduction / gamma-aminobutyric acid signaling pathway / SCF ubiquitin ligase complex / regulation of osteoblast differentiation / bone mineralization / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / negative regulation of potassium ion transport / ligase activity / Prolactin receptor signaling / positive regulation of transcription by RNA polymerase I / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of vascular endothelial growth factor production / general transcription initiation factor binding / negative regulation of T cell receptor signaling pathway / Response of EIF2AK4 (GCN2) to amino acid deficiency / cellular response to glucose starvation / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / ubiquitin-like ligase-substrate adaptor activity / endoplasmic reticulum unfolded protein response / protein K48-linked ubiquitination / nuclear periphery / gluconeogenesis / response to endoplasmic reticulum stress / dendrite membrane / cellular response to amino acid starvation / negative regulation of smoothened signaling pathway / MAP3K8 (TPL2)-dependent MAPK1/3 activation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / Deactivation of the beta-catenin transactivating complex / promoter-specific chromatin binding / 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 / regulation of synaptic plasticity / Degradation of GLI1 by the proteasome / response to nutrient levels / 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 / mRNA transcription by RNA polymerase II / Wnt signaling pathway / response to toxic substance / Degradation of beta-catenin by the destruction complex / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / neuron differentiation / protein polyubiquitination / Interleukin-1 signaling / sequence-specific double-stranded DNA binding / cellular response to UV / positive regulation of neuron apoptotic process / ubiquitin protein ligase activity / Regulation of PLK1 Activity at G2/M Transition / rhythmic process / transcription by RNA polymerase II / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia
Similarity search - Function
D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / bZIP transcription factor / 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 / : / bZIP transcription factor / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper 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
Cyclic AMP-dependent transcription factor ATF-4 / F-box/WD repeat-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 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 27, 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: Cyclic AMP-dependent transcription factor ATF-4


Theoretical massNumber of molelcules
Total (without water)43,2512
Polymers43,2512
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-9 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.986, 47.146, 150.913
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 Cyclic AMP-dependent transcription factor ATF-4 / cAMP-dependent transcription factor ATF-4 / Activating transcription factor 4 / Cyclic AMP- ...cAMP-dependent transcription factor ATF-4 / Activating transcription factor 4 / Cyclic AMP-responsive element-binding protein 2 / CREB-2 / cAMP-responsive element-binding protein 2 / Tax-responsive enhancer element-binding protein 67 / TaxREB67


Mass: 1421.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATF4, CREB2, TXREB / Production host: synthetic construct (others) / References: UniProt: P18848
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 1.85 Å3/Da / Density % sol: 33.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEGMME2K, 0.1 M Bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / 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: 1.996→75.456 Å / Num. obs: 16038 / % possible obs: 90.2 % / Redundancy: 7.4 % / CC1/2: 0.784 / Net I/σ(I): 6
Reflection shellResolution: 1.996→2.17 Å / Num. unique obs: 802 / CC1/2: 0.661

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.997→75.46 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.375 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.427 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 849 -RANDOM
Rwork0.1945 ---
obs0.1968 16038 71 %-
Displacement parametersBiso mean: 26.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.5724 Å20 Å20 Å2
2--0.2559 Å20 Å2
3----0.8283 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.997→75.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 0 148 3004
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082910HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043937HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1027SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes491HARMONIC5
X-RAY DIFFRACTIONt_it2910HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion382SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2480SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion16.81
LS refinement shellResolution: 2→2.11 Å
RfactorNum. reflection% reflection
Rfree0.2954 28 -
Rwork0.2546 --
obs0.2574 382 11.38 %

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