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- PDB-1zvd: Regulation of Smurf2 Ubiquitin Ligase Activity by Anchoring the E... -

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Basic information

Entry
Database: PDB / ID: 1zvd
TitleRegulation of Smurf2 Ubiquitin Ligase Activity by Anchoring the E2 to the HECT domain
ComponentsSmad ubiquitination regulatory factor 2
KeywordsLIGASE / Ubiquitin LigaseCatalytic Mechanism / x-ray crystal structure / TGFbeta
Function / homology
Function and homology information


positive regulation of trophoblast cell migration / regulation of transforming growth factor beta receptor signaling pathway / Signaling by BMP / HECT-type E3 ubiquitin transferase / Wnt signaling pathway, planar cell polarity pathway / SMAD binding / negative regulation of BMP signaling pathway / ubiquitin ligase complex / Downregulation of TGF-beta receptor signaling / Asymmetric localization of PCP proteins ...positive regulation of trophoblast cell migration / regulation of transforming growth factor beta receptor signaling pathway / Signaling by BMP / HECT-type E3 ubiquitin transferase / Wnt signaling pathway, planar cell polarity pathway / SMAD binding / negative regulation of BMP signaling pathway / ubiquitin ligase complex / Downregulation of TGF-beta receptor signaling / Asymmetric localization of PCP proteins / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / Ub-specific processing proteases / nuclear speck / membrane raft / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic 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 / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / C2 domain / C2 domain profile. / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / E3 ubiquitin-protein ligase SMURF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsOgunjimi, A.A. / Briant, D.J. / Pece-Barbara, N. / Le Roy, C. / Di Guglielmo, G.M. / Kavsak, P. / Rasmussen, R.K. / Seet, B.T. / Sicheri, F. / Wrana, J.L.
CitationJournal: Mol.Cell / Year: 2005
Title: Regulation of Smurf2 Ubiquitin Ligase Activity by Anchoring the E2 to the HECT Domain.
Authors: Ogunjimi, A.A. / Briant, D.J. / Pece-Barbara, N. / Le Roy, C. / Di Guglielmo, G.M. / Kavsak, P. / Rasmussen, R.K. / Seet, B.T. / Sicheri, F. / Wrana, J.L.
History
DepositionJun 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 28, 2011Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Smad ubiquitination regulatory factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9533
Polymers44,8351
Non-polymers1182
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.359, 70.509, 152.351
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 Smad ubiquitination regulatory factor 2 / Ubiquitin-- protein ligase SMURF2 / Smad-specific E3 ubiquitin ligase 2 / hSMURF2


Mass: 44835.168 Da / Num. of mol.: 1 / Fragment: HECT Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMURF2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9HAU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Sodium Phosphate, Potassium Phosphate, and Sodium Acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9799, 0.9997, 0.9568
DetectorDate: Apr 12, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97991
20.99971
30.95681
ReflectionResolution: 2.1→24.6 Å / Num. obs: 32394

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→24.57 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.337 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24792 1631 5 %RANDOM
Rwork0.20233 ---
all0.20463 ---
obs-30763 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 6 183 3278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223212
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.9544349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09223.929168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02815579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9351522
X-RAY DIFFRACTIONr_chiral_restr0.1410.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022470
X-RAY DIFFRACTIONr_nbd_refined0.2210.21418
X-RAY DIFFRACTIONr_nbtor_refined0.310.22156
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.211
X-RAY DIFFRACTIONr_mcbond_it1.2541.51876
X-RAY DIFFRACTIONr_mcangle_it2.2923041
X-RAY DIFFRACTIONr_scbond_it3.61431387
X-RAY DIFFRACTIONr_scangle_it5.6474.51304
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 116 -
Rwork0.253 1993 -
obs--87.58 %

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