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- PDB-2laz: Structure of the first WW domain of human Smurf1 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2laz
TitleStructure of the first WW domain of human Smurf1 in complex with a mono-phosphorylated human Smad1 derived peptide
Components
  • E3 ubiquitin-protein ligase SMURF1
  • Mothers against decapentaplegic homolog 1
KeywordsSIGNALING PROTEIN/TRANSCRIPTION / SMURF / SMAD / CDK / signal transduction / SIGNALING PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


substrate localization to autophagosome / mesodermal cell fate commitment / engulfment of target by autophagosome / homomeric SMAD protein complex / osteoblast fate commitment / SMAD protein complex / RUNX2 regulates bone development / heteromeric SMAD protein complex / co-SMAD binding / protein targeting to vacuole involved in autophagy ...substrate localization to autophagosome / mesodermal cell fate commitment / engulfment of target by autophagosome / homomeric SMAD protein complex / osteoblast fate commitment / SMAD protein complex / RUNX2 regulates bone development / heteromeric SMAD protein complex / co-SMAD binding / protein targeting to vacuole involved in autophagy / negative regulation of muscle cell differentiation / positive regulation of cartilage development / DEAD/H-box RNA helicase binding / primary miRNA binding / activin receptor binding / gamete generation / hindbrain development / ectoderm development / cardiac conduction system development / transforming growth factor beta receptor binding / primary miRNA processing / receptor catabolic process / positive regulation of dendrite extension / SMAD protein signal transduction / Signaling by BMP / embryonic pattern specification / negative regulation of activin receptor signaling pathway / HECT-type E3 ubiquitin transferase / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / nuclear inner membrane / Cardiogenesis / cartilage development / Wnt signaling pathway, planar cell polarity pathway / positive regulation of dendrite development / ureteric bud development / cardiac muscle cell proliferation / midbrain development / positive regulation of sprouting angiogenesis / SMAD binding / : / R-SMAD binding / negative regulation of BMP signaling pathway / anatomical structure morphogenesis / positive regulation of axon extension / BMP signaling pathway / positive regulation of osteoblast differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / transforming growth factor beta receptor signaling pathway / ossification / protein export from nucleus / male germ cell 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 / stem cell differentiation / negative regulation of transforming growth factor beta receptor signaling pathway / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / bone development / phospholipid binding / positive regulation of miRNA transcription / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / osteoblast differentiation / ubiquitin protein ligase activity / MAPK cascade / Antigen processing: Ubiquitination & Proteasome degradation / DNA-binding transcription activator activity, RNA polymerase II-specific / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / intracellular iron ion homeostasis / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / axon / negative regulation of cell population proliferation / neuronal cell body / DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain ...MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / E3 ubiquitin-protein ligase, SMURF1 type / SMAD-like domain superfamily / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / SMAD/FHA domain superfamily / 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
Mothers against decapentaplegic homolog 1 / E3 ubiquitin-protein ligase SMURF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMacias, M.J. / Aragon, E. / Goerner, N. / Zaromytidou, A. / Xi, Q. / Escobedo, A. / Massague, J.
CitationJournal: Genes Dev. / Year: 2011
Title: A Smad action turnover switch operated by WW domain readers of a phosphoserine code.
Authors: Aragon, E. / Goerner, N. / Zaromytidou, A.I. / Xi, Q. / Escobedo, A. / Massague, J. / Macias, M.J.
History
DepositionMar 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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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: Mothers against decapentaplegic homolog 1


Theoretical massNumber of molelcules
Total (without water)4,7922
Polymers4,7922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 300structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase SMURF1 / hSMURF1 / SMAD ubiquitination regulatory factor 1 / SMAD-specific E3 ubiquitin-protein ligase 1


Mass: 3878.220 Da / Num. of mol.: 1 / Fragment: residues 235-267
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, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Mothers against decapentaplegic homolog 1 / MAD homolog 1 / Mothers against DPP homolog 1 / JV4-1 / Mad-related protein 1 / SMAD family member ...MAD homolog 1 / Mothers against DPP homolog 1 / JV4-1 / Mad-related protein 1 / SMAD family member 1 / SMAD 1 / Smad1 / hSMAD1 / Transforming growth factor-beta-signaling protein 1 / BSP-1


Mass: 913.822 Da / Num. of mol.: 1 / Fragment: resdieus 210-217 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15797
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the first domain of human Smurf1 in complex with a phosphorylated human Smad1 derived peptide.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1333D CBCA(CO)NH
1433D HN(CA)CB
1522D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNEDD4LWW3-11
3 mMSMAD3-21
20 mMsodium phosphate-31
100 mMsodium chloride-41
2 mMsodium azide-51
1 mMNEDD4LWW3-6[U-100% 15N]2
3 mMSMAD3-72
20 mMsodium phosphate-82
100 mMsodium chloride-92
2 mMsodium azide-102
1 mMNEDD4LWW3-11[U-100% 13C; U-100% 15N]3
3 mMSMAD3-123
20 mMsodium phosphate-133
100 mMsodium chloride-143
2 mMsodium azide-153
Sample conditionsIonic strength: 0.42 / pH: 7 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 559 / NOE intraresidue total count: 0 / NOE long range total count: 219 / NOE medium range total count: 87 / NOE sequential total count: 180 / Hydrogen bond constraints total count: 10
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 300 / Conformers submitted total number: 24

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