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- PDB-2jqz: Solution Structure of the C2 domain of human Smurf2 -

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Basic information

Entry
Database: PDB / ID: 2jqz
TitleSolution Structure of the C2 domain of human Smurf2
ComponentsE3 ubiquitin-protein ligase SMURF2
KeywordsLIGASE / C2 domain / Smurf2 / Ubiquitin protein ligase / Phospholipid binding
Function / homology
Function and homology information


regulation of transforming growth factor beta receptor signaling pathway / positive regulation of trophoblast cell migration / Signaling by BMP / HECT-type E3 ubiquitin transferase / Wnt signaling pathway, planar cell polarity pathway / SMAD binding / negative regulation of BMP signaling pathway / ubiquitin ligase complex / Downregulation of TGF-beta receptor signaling / Asymmetric localization of PCP proteins ...regulation of transforming growth factor beta receptor signaling pathway / positive regulation of trophoblast cell migration / Signaling by BMP / HECT-type E3 ubiquitin transferase / Wnt signaling pathway, planar cell polarity pathway / SMAD binding / negative regulation of BMP signaling pathway / ubiquitin ligase complex / Downregulation of TGF-beta receptor signaling / Asymmetric localization of PCP proteins / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / protein ubiquitination / nuclear speck / membrane raft / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 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 / C2 domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase SMURF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsWiesner, S. / Ogunjimi, A.A. / Wang, H. / Rotin, D. / Sicheri, F. / Wrana, J.L. / Forman-Kay, J.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Autoinhibition of the HECT-Type Ubiquitin Ligase Smurf2 through Its C2 Domain
Authors: Wiesner, S. / Ogunjimi, A.A. / Wang, H.-R. / Rotin, D. / Sicheri, F. / Wrana, J.L. / Forman-Kay, J.D.
History
DepositionJun 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site
Revision 1.4May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SMURF2


Theoretical massNumber of molelcules
Total (without water)14,7021
Polymers14,7021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase SMURF2 / Smad ubiquitination regulatory factor 2 / Smad-specific E3 ubiquitin ligase 2 / hSMURF2


Mass: 14701.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMURF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus
References: UniProt: Q9HAU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1813D H(CCO)NH
1913D 1H-15N NOESY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM HEPES, 200 mM sodium chloride, 3 mM DTT, 0.03 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
220 mM hepes, 200 mM sodium chloride, 3 mM DTT, 0.03 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMHEPES1
200 mMsodium chloride1
3 mMDTT1
0.03 %sodium azide1
20 mMhepes2
200 mMsodium chloride2
3 mMDTT2
0.03 %sodium azide2
Sample conditionsIonic strength: 0.2 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
XEASYBartels et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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