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- PDB-9fsj: Crystal structure of the HECT domain of Smurf 1 in complex with i... -

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Basic information

Entry
Database: PDB / ID: 9fsj
TitleCrystal structure of the HECT domain of Smurf 1 in complex with inhibitor 8
ComponentsE3 ubiquitin-protein ligase SMURF1
KeywordsLIGASE / E3 ubiquitin-protein ligase SMURF1 / HECT domain / inhibitor / allosteric inhibition / BMP signaling / pulmonary vascular remodeling
Function / homology
Function and homology information


substrate localization to autophagosome / engulfment of target by autophagosome / protein targeting to vacuole involved in autophagy / activin receptor binding / ectoderm development / transforming growth factor beta receptor binding / receptor catabolic process / positive regulation of dendrite extension / Signaling by BMP / negative regulation of activin receptor signaling pathway ...substrate localization to autophagosome / engulfment of target by autophagosome / protein targeting to vacuole involved in autophagy / activin receptor binding / ectoderm development / transforming growth factor beta receptor binding / receptor catabolic process / positive regulation of dendrite extension / Signaling by BMP / negative regulation of activin receptor signaling pathway / HECT-type E3 ubiquitin transferase / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / Wnt signaling pathway, planar cell polarity pathway / SMAD binding / R-SMAD binding / negative regulation of BMP signaling pathway / positive regulation of axon extension / BMP signaling pathway / protein export from nucleus / Downregulation of TGF-beta receptor signaling / protein localization to plasma membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Asymmetric localization of PCP proteins / negative regulation of transforming growth factor beta receptor signaling pathway / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / phospholipid binding / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / axon / neuronal cell body / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain ...E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase SMURF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsOstermann, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2025
Title: Therapeutic potential of allosteric HECT E3 ligase inhibition.
Authors: Rothman, A.M.K. / Florentin, A. / Zink, F. / Quigley, C. / Bonneau, O. / Hemmig, R. / Hachey, A. / Rejtar, T. / Thaker, M. / Jain, R. / Huang, S.M. / Sutton, D. / Roger, J. / Zhang, J.H. / ...Authors: Rothman, A.M.K. / Florentin, A. / Zink, F. / Quigley, C. / Bonneau, O. / Hemmig, R. / Hachey, A. / Rejtar, T. / Thaker, M. / Jain, R. / Huang, S.M. / Sutton, D. / Roger, J. / Zhang, J.H. / Weiler, S. / Cotesta, S. / Ottl, J. / Srivastava, S. / Kordonsky, A. / Avishid, R. / Yariv, E. / Rathi, R. / Khvalevsky, O. / Troxler, T. / Binmahfooz, S.K. / Kleifeld, O. / Morrell, N.W. / Humbert, M. / Thomas, M.J. / Jarai, G. / Beckwith, R.E.J. / Cobb, J.S. / Smith, N. / Ostermann, N. / Tallarico, J. / Shaw, D. / Guth-Gundel, S. / Prag, G. / Rowlands, D.J.
History
DepositionJun 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SMURF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3472
Polymers43,9741
Non-polymers3721
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19280 Å2
Unit cell
Length a, b, c (Å)41.371, 91.447, 111.448
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase SMURF1 / hSMURF1 / HECT-type E3 ubiquitin transferase SMURF1 / SMAD ubiquitination regulatory factor 1 / ...hSMURF1 / HECT-type E3 ubiquitin transferase SMURF1 / SMAD ubiquitination regulatory factor 1 / SMAD-specific E3 ubiquitin-protein ligase 1


Mass: 43974.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMURF1, KIAA1625 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HCE7, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-TJQ / ethyl 5-[1,3-benzodioxol-5-ylmethyl(ethyl)carbamoyl]-2,4-dimethyl-1~{H}-pyrrole-3-carboxylate


Mass: 372.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG1500, 100 mM SPG pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→47.59 Å / Num. obs: 27310 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.3
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 0.7 / Num. unique obs: 1366

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→47.59 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.875 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.199
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1366 -RANDOM
Rwork0.2269 ---
obs0.2295 27310 100 %-
Displacement parametersBiso mean: 45.38 Å2
Baniso -1Baniso -2Baniso -3
1-3.4596 Å20 Å20 Å2
2---1.8234 Å20 Å2
3----1.6362 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.05→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 27 247 3316
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083147HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.94256HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1111SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes530HARMONIC5
X-RAY DIFFRACTIONt_it3147HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion382SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2675SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion18.76
LS refinement shellResolution: 2.05→2.06 Å
RfactorNum. reflection% reflection
Rfree0.4564 27 -
Rwork0.2951 --
obs0.3016 547 100 %

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