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- PDB-3pyc: Crystal structure of human SMURF1 C2 domain -

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Basic information

Entry
Database: PDB / ID: 3pyc
TitleCrystal structure of human SMURF1 C2 domain
ComponentsE3 ubiquitin-protein ligase SMURF1
KeywordsLIPID BINDING PROTEIN / phospholipid binding / membrane associate
Function / homology
Function and homology information


substrate localization to autophagosome / engulfment of target by autophagosome / protein targeting to vacuole involved in autophagy / activin receptor binding / ectoderm development / receptor catabolic process / transforming growth factor beta receptor binding / Signaling by BMP / positive regulation of dendrite extension / negative regulation of activin receptor signaling pathway ...substrate localization to autophagosome / engulfment of target by autophagosome / protein targeting to vacuole involved in autophagy / activin receptor binding / ectoderm development / receptor catabolic process / transforming growth factor beta receptor binding / Signaling by BMP / positive regulation of dendrite extension / negative regulation of activin receptor signaling pathway / positive regulation of ubiquitin-dependent protein catabolic process / HECT-type E3 ubiquitin transferase / I-SMAD binding / Wnt signaling pathway, planar cell polarity pathway / SMAD binding / R-SMAD binding / negative regulation of BMP signaling pathway / positive regulation of axon extension / BMP signaling pathway / protein export from nucleus / Downregulation of TGF-beta receptor signaling / 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 / phospholipid binding / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein ubiquitination / axon / neuronal cell body / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
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 / C2 domain / Protein kinase C conserved region 2 (CalB) / WW 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 SMURF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLi, X. / Li, P.
CitationJournal: To be Published
Title: Crystal structure of human SMURF1 C2 domain
Authors: Li, X. / Li, P.
History
DepositionDec 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0694
Polymers14,8411
Non-polymers2283
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.959, 47.048, 91.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14841.136 Da / Num. of mol.: 1 / Fragment: C2 domain, UNP residues 13-140
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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M HEPES (pH 6.5), 2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. all: 10154 / Num. obs: 10113 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→32.76 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.869 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24115 485 4.8 %RANDOM
Rwork0.20413 ---
obs0.20582 9586 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.774 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2---1.12 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.96→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 11 54 1103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221077
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9591459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20724.04347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53115196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.537157
X-RAY DIFFRACTIONr_chiral_restr0.140.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02790
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2442
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2716
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.251.5677
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05421070
X-RAY DIFFRACTIONr_scbond_it3.3523446
X-RAY DIFFRACTIONr_scangle_it5.3324.5387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.959→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 34 -
Rwork0.198 674 -
obs--96.59 %

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