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- PDB-2lb3: Structure of the WW domain of PIN1 in complex with a human phosph... -

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Basic information

Entry
Database: PDB / ID: 2lb3
TitleStructure of the WW domain of PIN1 in complex with a human phosphorylated Smad3 derived peptide
Components
  • Mothers against decapentaplegic homolog 2
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsSIGNALING PROTEIN/TRANSCRIPTION / PIN1 / SMAD / CDK / signal transduction / SIGNALING PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


paraxial mesoderm morphogenesis / zygotic specification of dorsal/ventral axis / activin responsive factor complex / nodal signaling pathway / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / SMAD protein complex / co-SMAD binding / heteromeric SMAD protein complex / determination of left/right asymmetry in lateral mesoderm ...paraxial mesoderm morphogenesis / zygotic specification of dorsal/ventral axis / activin responsive factor complex / nodal signaling pathway / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / SMAD protein complex / co-SMAD binding / heteromeric SMAD protein complex / determination of left/right asymmetry in lateral mesoderm / regulation of transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of cell cycle genes / odontoblast differentiation / trophoblast cell migration / secondary palate development / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / Transcriptional regulation of pluripotent stem cells / anterior/posterior pattern specification / Germ layer formation at gastrulation / cis-trans isomerase activity / primary miRNA processing / SMAD protein signal transduction / pulmonary valve morphogenesis / phosphothreonine residue binding / transforming growth factor beta receptor binding / Formation of definitive endoderm / Signaling by Activin / activin receptor signaling pathway / negative regulation of ossification / positive regulation of BMP signaling pathway / type I transforming growth factor beta receptor binding / Formation of axial mesoderm / ureteric bud development / Signaling by NODAL / endocardial cushion morphogenesis / negative regulation of cell motility / mesoderm formation / regulation of protein localization to nucleus / response to cholesterol / negative regulation of brown fat cell differentiation / I-SMAD binding / mitogen-activated protein kinase kinase binding / aortic valve morphogenesis / GTPase activating protein binding / ubiquitin ligase activator activity / : / regulation of mitotic nuclear division / protein peptidyl-prolyl isomerization / cell fate commitment / negative regulation of SMAD protein signal transduction / SMAD binding / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / R-SMAD binding / TGF-beta receptor signaling activates SMADs / negative regulation of cell differentiation / cytoskeletal motor activity / Rho protein signal transduction / gastrulation / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / anatomical structure morphogenesis / positive regulation of epithelial to mesenchymal transition / postsynaptic cytosol / phosphatase binding / cis-regulatory region sequence-specific DNA binding / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of cytokinesis / Downregulation of TGF-beta receptor signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein catabolic process / regulation of protein stability / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / negative regulation of ERK1 and ERK2 cascade / Downregulation of SMAD2/3:SMAD4 transcriptional activity / protein destabilization / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / synapse organization / positive regulation of protein phosphorylation / beta-catenin binding / tau protein binding / ISG15 antiviral mechanism / disordered domain specific binding / positive regulation of canonical Wnt signaling pathway / regulation of gene expression / neuron differentiation / transcription regulator complex / ciliary basal body / double-stranded DNA binding / midbody / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / response to hypoxia
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 / SMAD-like domain superfamily / : / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / SMAD/FHA domain superfamily / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / SMAD family member 2
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 1.2Nov 6, 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

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
B: Mothers against decapentaplegic homolog 2


Theoretical massNumber of molelcules
Total (without water)5,1192
Polymers5,1192
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)20 / 300structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1


Mass: 4231.692 Da / Num. of mol.: 1 / Fragment: residues 6-41
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Protein/peptide Mothers against decapentaplegic homolog 2 / MAD homolog 2 / Mothers against DPP homolog 2 / JV18-1 / Mad-related protein 2 / hMAD-2 / SMAD ...MAD homolog 2 / Mothers against DPP homolog 2 / JV18-1 / Mad-related protein 2 / hMAD-2 / SMAD family member 2 / SMAD 2 / Smad2 / hSMAD2


Mass: 886.882 Da / Num. of mol.: 1 / Fragment: residues 176-183 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15796
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 PIN1 in complex with a human Smad3 derived peptide( resi 173-186).
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: 557 / NOE intraresidue total count: 0 / NOE long range total count: 215 / NOE medium range total count: 56 / NOE sequential total count: 167 / 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: 20

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