[English] 日本語
Yorodumi
- PDB-9tes: Crystal structure of beta-TrCP bound by diphosphorylated PDCD4 de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9tes
TitleCrystal structure of beta-TrCP bound by diphosphorylated PDCD4 degron peptide
Components
  • F-box/WD repeat-containing protein 1A
  • Programmed cell death protein 4
KeywordsTRANSFERASE / E3 ligase / phosphodegron / beta-TrCP / i-kappa-B-alpha
Function / homology
Function and homology information


epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / protein phosphorylated amino acid binding / negative regulation of JUN kinase activity / regulation of cell cycle process / positive regulation of circadian rhythm / ubiquitin ligase activator activity / regulation of canonical Wnt signaling pathway / protein dephosphorylation ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / protein phosphorylated amino acid binding / negative regulation of JUN kinase activity / regulation of cell cycle process / positive regulation of circadian rhythm / ubiquitin ligase activator activity / regulation of canonical Wnt signaling pathway / protein dephosphorylation / positive regulation of vascular associated smooth muscle cell apoptotic process / 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 vascular associated smooth muscle cell proliferation / BMP signaling pathway / positive regulation of endothelial cell apoptotic process / negative regulation of T cell receptor signaling pathway / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / negative regulation of cytokine production involved in inflammatory response / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / 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 / positive regulation of non-canonical NF-kappaB signal transduction / 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 / ubiquitin protein ligase activity / Regulation of PLK1 Activity at G2/M Transition / rhythmic process / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to lipopolysaccharide / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein dimerization activity / protein ubiquitination / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / Programmed cell death protein 4 / : / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / A Receptor for Ubiquitination Targets / Domain in DAP-5, eIF4G, MA-3 and other proteins. ...D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / Programmed cell death protein 4 / : / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / A Receptor for Ubiquitination Targets / Domain in DAP-5, eIF4G, MA-3 and other proteins. / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain / WD domain, G-beta repeat / Armadillo-type fold / 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
Programmed cell death protein 4 / F-box/WD repeat-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.217 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 26, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F-box/WD repeat-containing protein 1A
B: Programmed cell death protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4024
Polymers43,3162
Non-polymers862
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-10 kcal/mol
Surface area15360 Å2
Unit cell
Length a, b, c (Å)44.719, 46.971, 150.861
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
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 Programmed cell death protein 4 / Neoplastic transformation inhibitor protein / Nuclear antigen H731-like / Protein 197/15a


Mass: 1486.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD4, H731 / Production host: synthetic construct (others) / References: UniProt: Q53EL6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG10K, 0.1 M Na-Hepes pH 7.5

-
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: 1.217→75.43 Å / Num. obs: 84489 / % possible obs: 91.6 % / Redundancy: 7.7 % / CC1/2: 0.999 / Net I/σ(I): 9.8
Reflection shellResolution: 1.217→1.277 Å / Num. unique obs: 4224 / CC1/2: 0.653

-
Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.217→75.43 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.059
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 4259 -RANDOM
Rwork0.2122 ---
obs0.2136 84489 87.8 %-
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.2044 Å20 Å20 Å2
2---0.2303 Å20 Å2
3---0.0259 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.217→75.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 5 228 3120
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0142953HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.283994HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1048SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes499HARMONIC5
X-RAY DIFFRACTIONt_it2953HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion384SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2771SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.56
X-RAY DIFFRACTIONt_other_torsion14.23
LS refinement shellResolution: 1.22→1.26 Å
RfactorNum. reflection% reflection
Rfree0.268 88 -
Rwork0.2758 --
obs0.2754 1690 18.71 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more