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- PDB-7m3q: Structure of the Smurf2 HECT Domain with a High Affinity Ubiquiti... -

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Basic information

Entry
Database: PDB / ID: 7m3q
TitleStructure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV)
Components
  • E3 ubiquitin-protein ligase SMURF2
  • Ubiquitin variant
KeywordsSIGNALING PROTEIN/TRANSFERASE / High-affinity / SIGNALING PROTEIN / SIGNALING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


regulation of transforming growth factor beta receptor signaling pathway / positive regulation of trophoblast cell migration / Signaling by BMP / HECT-type E3 ubiquitin transferase / Wnt signaling pathway, planar cell polarity pathway / SMAD binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / negative regulation of BMP signaling pathway ...regulation of transforming growth factor beta receptor signaling pathway / positive regulation of trophoblast cell migration / Signaling by BMP / HECT-type E3 ubiquitin transferase / Wnt signaling pathway, planar cell polarity pathway / SMAD binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / negative regulation of BMP signaling pathway / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / ubiquitin ligase complex / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / cytosolic ribosome / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / 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. ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / 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 / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / C2 domain superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Ubiquitin-ribosomal protein eL40 fusion protein / E3 ubiquitin-protein ligase SMURF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChowdhury, A. / Singer, A.U. / Ogunjimi, A.A. / Teyra, J. / Zhang, W. / Sicheri, F. / Sidhu, S.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Ontario Research Fund72056614 Canada
CitationJournal: To be published
Title: Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV)
Authors: Chowdhury, A. / Singer, A.U. / Ogunjimi, A.A. / Teyra, J. / Chung, J. / Wrana, J.L. / Zhang, W. / Sicheri, F. / Sachdev, S.S.
History
DepositionMar 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SMURF2
B: Ubiquitin variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,44114
Polymers56,7742
Non-polymers66712
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-91 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.530, 72.068, 48.813
Angle α, β, γ (deg.)90.000, 94.607, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein E3 ubiquitin-protein ligase SMURF2 / hSMURF2 / HECT-type E3 ubiquitin transferase SMURF2 / SMAD ubiquitination regulatory factor 2 / ...hSMURF2 / HECT-type E3 ubiquitin transferase SMURF2 / SMAD ubiquitination regulatory factor 2 / SMAD-specific E3 ubiquitin-protein ligase 2


Mass: 45254.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMURF2 / Plasmid: pProEX-HTa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9HAU4, HECT-type E3 ubiquitin transferase
#2: Protein Ubiquitin variant


Mass: 11519.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA52, UBCEP2 / Plasmid: pET53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62987

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Non-polymers , 6 types, 66 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: 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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Details

Has ligand of interestN
Has protein modificationN

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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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.5 M Ammonium Sulphate and 100 mM MES pH 6.0. Trypsin was added to the protein complex at a final concentration of 10 microgram per mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2020 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.45→67.83 Å / Num. obs: 24895 / % possible obs: 97.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 54.49 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.8
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2871 / CC1/2: 0.478 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZVD and Swiss Model of Ubiquitin Variant

1zvd


Resolution: 2.5→67.83 Å / SU ML: 0.3266 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 1201 4.99 %
Rwork0.2029 22875 -
obs0.2045 24076 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.6 Å2
Refinement stepCycle: LAST / Resolution: 2.5→67.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 30 54 3699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883763
X-RAY DIFFRACTIONf_angle_d1.14445099
X-RAY DIFFRACTIONf_chiral_restr0.0635554
X-RAY DIFFRACTIONf_plane_restr0.008656
X-RAY DIFFRACTIONf_dihedral_angle_d24.58521391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.30831300.26662544X-RAY DIFFRACTION99.55
2.6-2.720.24811500.252544X-RAY DIFFRACTION99.67
2.72-2.860.27631350.25682522X-RAY DIFFRACTION99.77
2.86-3.040.38461380.29172533X-RAY DIFFRACTION99.48
3.04-3.280.27771160.25542552X-RAY DIFFRACTION98.96
3.28-3.610.25281300.22462519X-RAY DIFFRACTION98.81
3.61-4.130.23041450.18782529X-RAY DIFFRACTION98.67
4.13-5.20.19211470.15672516X-RAY DIFFRACTION98.45
5.2-67.830.18381100.17352616X-RAY DIFFRACTION97.92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3739-0.2352-1.8310.5486-0.14981.41930.1546-0.22840.1630.0483-0.01930.1393-0.01790.0312-0.1520.3931-0.008-0.07690.3796-0.04280.384932.414411.209913.9135
27.70061.53183.70882.85041.22914.8745-0.09850.221-0.179-0.36450.0702-0.3915-0.05050.18350.00520.41770.04280.04110.24980.04760.458.33635.908130.4432
31.4192-1.92242.40012.5906-3.24034.0244-0.6171-1.23341.0037-0.0670.8104-1.4154-1.64782.00860.11720.763-0.28870.16031.4801-0.75151.662916.383227.468734.902
45.4255-0.78161.64478.92954.26182.7892-0.303-0.90641.8960.1440.9159-1.2577-1.8581.3887-0.4410.9772-0.2220.19811.017-0.46231.355510.214728.475731.9372
5-0.00110.00240.00080.03710.01080.00010.707-1.34760.53971.1383-0.5177-0.8998-0.2420.309-0.20381.1196-0.1699-0.23482.4224-0.96082.049917.397132.169547.3126
66.7807-0.74581.274.7895-0.5115.0249-0.0539-1.58731.26271.10930.52890.5975-1.74150.775-0.46961.1773-0.13340.32051.5436-0.75051.54618.301132.412842.3333
74.4453-1.3111.55924.699-1.86866.95830.5169-1.56452.0412-0.10950.42440.5031-0.39161.0895-1.01530.6802-0.09380.15181.5414-0.39351.40123.483425.989340.2266
89.8485-4.5256-1.17878.6945-1.85034.1396-0.981-2.52710.93421.71381.1255-0.5258-0.44541.4219-0.19071.02090.1486-0.15371.7023-0.23320.870712.664518.973446.3286
92.54462.6429-2.29118.34143.06667.37120.9103-2.6541-0.48581.09070.2776-1.6068-1.09350.9018-1.23411.1213-0.0397-0.31582.1015-0.52171.274120.436223.392544.7886
105.47274.2521-1.10274.021-1.34280.5611.0531-0.70360.90.63710.2264-0.679-0.40160.7443-1.01510.6966-0.28590.1781.6186-0.5971.10794.985821.128838.1401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 369 through 618 )
2X-RAY DIFFRACTION2chain 'A' and (resid 619 through 741 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 7 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 16 )
5X-RAY DIFFRACTION5chain 'B' and (resid 17 through 22 )
6X-RAY DIFFRACTION6chain 'B' and (resid 23 through 33 )
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 44 )
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 74 )

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