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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


zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / endoderm formation ...zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / endoderm formation / co-SMAD binding / heteromeric SMAD protein complex / odontoblast differentiation / determination of left/right asymmetry in lateral mesoderm / secondary palate development / pericardium development / FOXO-mediated transcription of cell cycle genes / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / Transcriptional regulation of pluripotent stem cells / cis-trans isomerase activity / regulation of transforming growth factor beta receptor signaling pathway / embryonic foregut morphogenesis / phosphothreonine residue binding / transforming growth factor beta receptor binding / primary miRNA processing / Germ layer formation at gastrulation / pulmonary valve morphogenesis / signal transduction involved in regulation of gene expression / type I transforming growth factor beta receptor binding / negative regulation of cell motility / Formation of definitive endoderm / activin receptor signaling pathway / ubiquitin ligase activator activity / Signaling by Activin / Formation of axial mesoderm / positive regulation of BMP signaling pathway / SMAD protein signal transduction / Signaling by NODAL / embryonic cranial skeleton morphogenesis / response to cholesterol / regulation of protein localization to nucleus / I-SMAD binding / pancreas development / aortic valve morphogenesis / GTPase activating protein binding / insulin secretion / ureteric bud development / anterior/posterior pattern specification / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / endocardial cushion morphogenesis / regulation of mitotic nuclear division / organ growth / adrenal gland development / negative regulation of amyloid-beta formation / negative regulation of SMAD protein signal transduction / SMAD binding / PI5P Regulates TP53 Acetylation / TGF-beta receptor signaling activates SMADs / R-SMAD binding / cytoskeletal motor activity / mesoderm formation / RHO GTPases Activate NADPH Oxidases / gastrulation / phosphoserine residue binding / anatomical structure morphogenesis / positive regulation of epithelial to mesenchymal transition / phosphatase binding / cell fate commitment / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cis-regulatory region sequence-specific DNA binding / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / Downregulation of TGF-beta receptor signaling / post-embryonic development / transforming growth factor beta receptor signaling pathway / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / synapse organization / phosphoprotein binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / lung development / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / tau protein binding / regulation of protein stability / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / neuron differentiation / beta-catenin binding / positive regulation of GTPase activity / positive regulation of canonical Wnt signaling pathway
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 / WW domain / SMAD/FHA domain superfamily / 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 / Mothers against decapentaplegic homolog 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

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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
Water0
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

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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: 0.420 / 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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