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- PDB-9fsk: Crystal structure of the HECT domain of Smurf1 -

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Basic information

Entry
Database: PDB / ID: 9fsk
TitleCrystal structure of the HECT domain of Smurf1
ComponentsE3 ubiquitin-protein ligase SMURF1
KeywordsLIGASE / HECT-type E3 ligase / 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: 2.75 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

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SMURF1
B: E3 ubiquitin-protein ligase SMURF1
C: E3 ubiquitin-protein ligase SMURF1
D: E3 ubiquitin-protein ligase SMURF1


Theoretical massNumber of molelcules
Total (without water)175,8974
Polymers175,8974
Non-polymers00
Water3,531196
1
A: E3 ubiquitin-protein ligase SMURF1


Theoretical massNumber of molelcules
Total (without water)43,9741
Polymers43,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase SMURF1


Theoretical massNumber of molelcules
Total (without water)43,9741
Polymers43,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase SMURF1


Theoretical massNumber of molelcules
Total (without water)43,9741
Polymers43,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase SMURF1


Theoretical massNumber of molelcules
Total (without water)43,9741
Polymers43,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.157, 74.318, 161.063
Angle α, β, γ (deg.)90, 111.93, 90
Int Tables number5
Space group name H-MC121

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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.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25 % PEG 3350, 0.1 M Bis Tris pH 5.9, 0.2 M MgCl2, 0.02 M NH4OAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→78.92 Å / Num. obs: 48367 / % possible obs: 98.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.8
Reflection shellResolution: 2.75→2.77 Å / Rmerge(I) obs: 0.6 / Num. unique obs: 2419

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→78.92 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.848 / Cross valid method: THROUGHOUT / SU R Blow DPI: 3.547 / SU Rfree Blow DPI: 0.406
RfactorNum. reflection% reflectionSelection details
Rfree0.3013 2419 -RANDOM
Rwork0.2485 ---
obs0.2512 48367 98.9 %-
Displacement parametersBiso mean: 69.12 Å2
Baniso -1Baniso -2Baniso -3
1--6.8858 Å20 Å2-2.4613 Å2
2--12.4974 Å20 Å2
3----5.6116 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.75→78.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12110 0 0 196 12306
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812412HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9516781HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4389SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2096HARMONIC5
X-RAY DIFFRACTIONt_it12412HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1522SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9401SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion21.48
LS refinement shellResolution: 2.75→2.77 Å
RfactorNum. reflection% reflection
Rfree0.4142 49 -
Rwork0.315 --
obs0.3199 968 99.59 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67230.1943-0.27162.93120.19080.53910.0481-0.0064-0.0377-0.0064-0.02840.003-0.03770.003-0.0197-0.20230.04-0.05-0.10860.0074-0.048514.82793.152823.6808
21.11420.01060.03195.16250.94170.5631-0.0157-0.3713-0.0143-0.3713-0.02470.0205-0.01430.02050.0404-0.1567-0.0192-0.1411-0.2140.0565-0.09736.5311-13.369753.3192
33.20960.0364-1.06644.13930.94382.137-0.0337-0.5597-0.2268-0.5597-0.0745-0.1516-0.2268-0.15160.1082-0.2566-0.05230.0336-0.1532-0.0107-0.036925.60333.7559-15.3741
42.3746-0.5118-2.05294.21792.45122.97690.1966-0.2618-0.1775-0.26180.06530.0382-0.17750.0382-0.2619-0.2213-0.11880.1415-0.25120.0715-0.078177.5352-14.673754.86
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A377 - 750
2X-RAY DIFFRACTION2{ B|* }B377 - 750
3X-RAY DIFFRACTION3{ C|* }C377 - 750
4X-RAY DIFFRACTION4{ D|* }D377 - 750

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