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- PDB-2lb1: Structure of the second domain of human Smurf1 in complex with a ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2lb1 | ||||||
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Title | Structure of the second domain of human Smurf1 in complex with a human Smad1 derived peptide | ||||||
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![]() | SIGNALING PROTEIN/TRANSCRIPTION / SMURF / SMAD / CDK / signal transduction / SIGNALING PROTEIN-TRANSCRIPTION complex | ||||||
Function / homology | ![]() 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 / co-SMAD binding / heteromeric SMAD protein complex / 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 / co-SMAD binding / heteromeric SMAD protein complex / protein targeting to vacuole involved in autophagy / negative regulation of muscle cell differentiation / positive regulation of cartilage development / primary miRNA binding / DEAD/H-box RNA helicase binding / activin receptor binding / gamete generation / hindbrain development / ectoderm development / cardiac conduction system development / receptor catabolic process / primary miRNA processing / transforming growth factor beta receptor binding / Signaling by BMP / positive regulation of dendrite extension / embryonic pattern specification / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / positive regulation of ubiquitin-dependent protein catabolic process / HECT-type E3 ubiquitin transferase / I-SMAD binding / cartilage development / Cardiogenesis / Wnt signaling pathway, planar cell polarity pathway / nuclear inner membrane / cardiac muscle cell proliferation / ureteric bud development / midbrain development / homeostatic process / positive regulation of sprouting angiogenesis / SMAD binding / R-SMAD binding / cellular response to organic cyclic compound / negative regulation of BMP signaling pathway / anatomical structure morphogenesis / positive regulation of axon extension / BMP signaling pathway / positive regulation of osteoblast differentiation / protein export from nucleus / Downregulation of TGF-beta receptor signaling / ossification / transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Asymmetric localization of PCP proteins / protein localization to plasma membrane / negative regulation of transforming growth factor beta receptor signaling pathway / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / bone development / phospholipid binding / positive regulation of miRNA transcription / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / MAPK cascade / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / protein ubiquitination / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / axon / DNA-templated transcription / neuronal cell body / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Macias, M.J. / Aragon, E. / Goerner, N. / Zaromytidou, A. / Xi, Q. / Escobedo, A. / Massague, J. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.2 KB | Display | ![]() |
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PDB format | ![]() | 254.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.4 KB | Display | ![]() |
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Full document | ![]() | 618.6 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2lajC ![]() 2lawC ![]() 2laxC ![]() 2layC ![]() 2lazC ![]() 2lb0C ![]() 2lb2C ![]() 2lb3C C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 4170.647 Da / Num. of mol.: 1 / Fragment: residues 305-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9HCE7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein/peptide | Mass: 1477.592 Da / Num. of mol.: 1 / Fragment: residues 221-233 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Structure of the first domain of human Smurf1 in complex with a human Smad1 derived peptide. | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample conditions | Ionic strength: 0.420 / pH: 7 / Pressure: ambient / Temperature: 285 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 711 / NOE intraresidue total count: 0 / NOE long range total count: 308 / NOE medium range total count: 51 / NOE sequential total count: 171 / Hydrogen bond constraints total count: 10 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 300 / Conformers submitted total number: 20 |