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- PDB-6fx4: Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C -

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Basic information

Entry
Database: PDB / ID: 6fx4
TitleDisulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C
Components
  • E3 ubiquitin-protein ligase SMURF2
  • Polyubiquitin-B
KeywordsLIGASE / E3 HECT ligase / Ubiquitin transfer
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 / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / Wnt signaling pathway, planar cell polarity pathway / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development ...positive regulation of trophoblast cell migration / regulation of transforming growth factor beta receptor signaling pathway / Signaling by BMP / HECT-type E3 ubiquitin transferase / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / Wnt signaling pathway, planar cell polarity pathway / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / SMAD binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of BMP signaling pathway / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / 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) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / neuron projection morphogenesis / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / Evasion by RSV of host interferon responses / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
Similarity search - Function
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) ...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. / 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 / 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
Polyubiquitin-B / E3 ubiquitin-protein ligase SMURF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsJaeckl, M. / Holdermann, I. / Wiesner, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J. Mol. Biol. / Year: 2018
Title: beta-Sheet Augmentation Is a Conserved Mechanism of Priming HECT E3 Ligases for Ubiquitin Ligation.
Authors: Jackl, M. / Stollmaier, C. / Strohaker, T. / Hyz, K. / Maspero, E. / Polo, S. / Wiesner, S.
History
DepositionMar 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Structure summary / Category: audit_author
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / struct ...entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.symmetry
Revision 1.4Jan 17, 2024Group: 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

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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: Polyubiquitin-B
C: E3 ubiquitin-protein ligase SMURF2
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3206
Polymers45,1354
Non-polymers1842
Water1,51384
1
A: E3 ubiquitin-protein ligase SMURF2
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6603
Polymers22,5682
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-6 kcal/mol
Surface area10140 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase SMURF2
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6603
Polymers22,5682
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-6 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.630, 45.950, 70.460
Angle α, β, γ (deg.)108.920, 94.430, 106.750
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 116)
21(chain C and resid 2 through 116)
12chain B
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 2 through 116)A2 - 116
211(chain C and resid 2 through 116)C2 - 116
112chain BB1 - 76
212chain DD1 - 76

NCS ensembles :
ID
1
2

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Components

#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: 13944.820 Da / Num. of mol.: 2 / Mutation: C646A, C706N, C743S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMURF2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HAU4, HECT-type E3 ubiquitin transferase
#2: Protein Polyubiquitin-B


Mass: 8622.922 Da / Num. of mol.: 2 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.998 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 2.3→42.341 Å / Num. all: 18696 / Num. obs: 18696 / % possible obs: 97.6 % / Redundancy: 2 % / Biso Wilson estimate: 28.89 Å2 / Rpim(I) all: 0.17 / Rrim(I) all: 0.254 / Rsym value: 0.185 / Net I/av σ(I): 4 / Net I/σ(I): 3.4 / Num. measured all: 36906
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.3-2.4220.7331.127030.7651.140.73395.7
2.42-2.5720.5551.425570.5670.8470.55597.2
2.57-2.751.90.5331.424030.4690.7020.53397.1
2.75-2.971.90.3652.222830.330.4940.36597.9
2.97-3.2520.255320760.2350.350.25598
3.25-3.6420.1674.518820.1560.2330.16798.3
3.64-4.21.90.1096.416840.1010.150.10998.1
4.2-5.1420.076914110.0720.1070.07698.7
5.14-7.2720.0898.110930.0850.1270.08998.6
7.27-42.34120.04115.16040.0410.0620.04199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.81 Å19.57 Å
Translation4.81 Å19.57 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zvd, 4bbn

1zvd

4bbn


Resolution: 2.5→19.566 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.18
RfactorNum. reflection% reflection
Rfree0.239 734 5 %
Rwork0.1873 --
obs0.1899 14670 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.52 Å2 / Biso mean: 39.1772 Å2 / Biso min: 9.43 Å2
Refinement stepCycle: final / Resolution: 2.5→19.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 12 84 3204
Biso mean--40.48 31.99 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023181
X-RAY DIFFRACTIONf_angle_d0.5684296
X-RAY DIFFRACTIONf_chiral_restr0.043480
X-RAY DIFFRACTIONf_plane_restr0.004552
X-RAY DIFFRACTIONf_dihedral_angle_d15.0661941
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1098X-RAY DIFFRACTION7.112TORSIONAL
12C1098X-RAY DIFFRACTION7.112TORSIONAL
21B754X-RAY DIFFRACTION7.112TORSIONAL
22D754X-RAY DIFFRACTION7.112TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.69260.33071460.2572775292198
2.6926-2.96280.30031480.23712810295898
2.9628-3.38960.24981460.20422768291498
3.3896-4.26320.21181470.16752791293899
4.2632-19.56650.19861470.15122792293999
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)
12.23290.1158-0.05842.96240.54551.3297-0.10680.17590.0116-0.31110.02120.3715-0.0359-0.05870.06380.1884-0.0273-0.01490.18280.00060.2165-17.5752-37.849710.4096
20.9104-0.01680.10021.1418-0.11353.14610.0353-0.2752-0.09820.3431-0.02850.0110.36140.38530.00730.45990.00220.0020.35180.05510.2779-8.0493-42.038336.0733
32.92880.28760.54882.29170.25711.62840.0514-0.15240.0170.07040.0223-0.11410.10220.006-0.05390.1727-0.00070.0090.1881-0.0190.24080.633-18.925921.545
41.1038-0.0166-0.12990.73450.19653.70920.00110.44240.1052-0.4119-0.01720.07230.1261-0.78890.050.4444-0.0182-0.00440.48520.00520.2693-8.9054-13.019-3.3228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 116)A1 - 116
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 76)B1 - 76
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 118)C2 - 118
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 76)D1 - 76

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