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- PDB-5hpt: System-wide modulation of HECT E3 ligases with selective ubiquiti... -

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Basic information

Entry
Database: PDB / ID: 5hpt
TitleSystem-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7
Components
  • NEDD4-like E3 ubiquitin-protein ligase WWP1
  • Ubiquitin variant P2.3
  • Ubiquitin-conjugating enzyme E2 L3
KeywordsLIGASE/TRANSFERASE / HECT E3 / WWP1 / Ubiquitin / Ubv / UBCH7 / LIGASE-TRANSFERASE complex
Function / homology
Function and homology information


cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / HECT-type E3 ubiquitin transferase / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / Peptide chain elongation ...cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / HECT-type E3 ubiquitin transferase / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / Peptide chain elongation / Selenocysteine synthesis / ubiquitin conjugating enzyme activity / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / monoatomic ion transmembrane transport / 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 / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / 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 / 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) / 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 / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / central nervous system development / 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
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 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / C2 domain / Protein kinase C conserved region 2 (CalB) ...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 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / C2 domain / Protein kinase C conserved region 2 (CalB) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Ubiquitin-conjugating enzyme/RWD-like / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eL40 fusion protein / Ubiquitin-conjugating enzyme E2 L3 / NEDD4-like E3 ubiquitin-protein ligase WWP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsWu, K.-P. / Schulman, B.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: Mol.Cell / Year: 2016
Title: System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.
Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / ...Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / Sheng, Y. / Hao, Z. / Li, Y. / Brown, K.R. / Lemichez, E. / Chen, J. / Tong, Y. / Harper, J.W. / Moffat, J. / Rotin, D. / Schulman, B.A. / Sidhu, S.S.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEDD4-like E3 ubiquitin-protein ligase WWP1
B: Ubiquitin variant P2.3
C: Ubiquitin-conjugating enzyme E2 L3
D: NEDD4-like E3 ubiquitin-protein ligase WWP1
E: Ubiquitin variant P2.3
F: Ubiquitin-conjugating enzyme E2 L3
G: NEDD4-like E3 ubiquitin-protein ligase WWP1
H: Ubiquitin variant P2.3


Theoretical massNumber of molelcules
Total (without water)200,9128
Polymers200,9128
Non-polymers00
Water905
1
A: NEDD4-like E3 ubiquitin-protein ligase WWP1
B: Ubiquitin variant P2.3
C: Ubiquitin-conjugating enzyme E2 L3


Theoretical massNumber of molelcules
Total (without water)73,2043
Polymers73,2043
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-25 kcal/mol
Surface area28740 Å2
MethodPISA
2
D: NEDD4-like E3 ubiquitin-protein ligase WWP1
E: Ubiquitin variant P2.3
F: Ubiquitin-conjugating enzyme E2 L3


Theoretical massNumber of molelcules
Total (without water)73,2043
Polymers73,2043
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-23 kcal/mol
Surface area29260 Å2
MethodPISA
3
G: NEDD4-like E3 ubiquitin-protein ligase WWP1
H: Ubiquitin variant P2.3


Theoretical massNumber of molelcules
Total (without water)54,5032
Polymers54,5032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-17 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.005, 118.897, 158.663
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 NEDD4-like E3 ubiquitin-protein ligase WWP1 / Atrophin-1-interacting protein 5 / AIP5 / TGIF-interacting ubiquitin ligase 1 / Tiul1 / WW domain- ...Atrophin-1-interacting protein 5 / AIP5 / TGIF-interacting ubiquitin ligase 1 / Tiul1 / WW domain-containing protein 1


Mass: 45134.609 Da / Num. of mol.: 3 / Fragment: HECT domain (UNP residues 537-917)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9H0M0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Ubiquitin variant P2.3


Mass: 9368.444 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62987*PLUS
#3: Protein Ubiquitin-conjugating enzyme E2 L3 / E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin- ...E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3


Mass: 18701.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P68036, E2 ubiquitin-conjugating enzyme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: isopropanol 10%, PEG3350 8%, sodium citrate 0.1 M / PH range: 5.0-5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.84→95.15 Å / Num. obs: 97828 / % possible obs: 99.86 % / Redundancy: 6.7 % / Net I/σ(I): 15.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ND7

1nd7


Resolution: 2.84→95.146 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.24
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3811 3.9 %RANDOM
Rwork0.2183 ---
obs0.219 97828 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.84→95.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13524 0 0 5 13529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113850
X-RAY DIFFRACTIONf_angle_d1.61218686
X-RAY DIFFRACTIONf_dihedral_angle_d16.7245228
X-RAY DIFFRACTIONf_chiral_restr0.0671983
X-RAY DIFFRACTIONf_plane_restr0.0072394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.8760.37281570.35633446X-RAY DIFFRACTION99
2.876-2.91380.30261440.333491X-RAY DIFFRACTION100
2.9138-2.95370.39211280.31933497X-RAY DIFFRACTION100
2.9537-2.99590.31221430.31033535X-RAY DIFFRACTION100
2.9959-3.04070.32351430.31793458X-RAY DIFFRACTION100
3.0407-3.08820.32541210.30373509X-RAY DIFFRACTION100
3.0882-3.13880.36651370.31813512X-RAY DIFFRACTION100
3.1388-3.19290.35781640.30573424X-RAY DIFFRACTION100
3.1929-3.2510.33951290.28723564X-RAY DIFFRACTION100
3.251-3.31350.24521480.26343410X-RAY DIFFRACTION98
3.3135-3.38120.28281270.25563481X-RAY DIFFRACTION99
3.3812-3.45470.29991520.25083487X-RAY DIFFRACTION100
3.4547-3.53510.22961390.2373485X-RAY DIFFRACTION100
3.5351-3.62350.22021400.23023522X-RAY DIFFRACTION100
3.6235-3.72140.2431480.21563442X-RAY DIFFRACTION100
3.7214-3.8310.21781450.21573535X-RAY DIFFRACTION100
3.831-3.95460.19921510.2193450X-RAY DIFFRACTION99
3.9546-4.0960.2791330.20583452X-RAY DIFFRACTION99
4.096-4.260.22431400.19553499X-RAY DIFFRACTION99
4.26-4.45380.22051370.18813470X-RAY DIFFRACTION100
4.4538-4.68860.22241450.17943483X-RAY DIFFRACTION100
4.6886-4.98240.20531390.17993505X-RAY DIFFRACTION100
4.9824-5.3670.19511370.1873439X-RAY DIFFRACTION99
5.367-5.90710.21391560.213493X-RAY DIFFRACTION100
5.9071-6.76160.2331280.21113495X-RAY DIFFRACTION100
6.7616-8.51810.23051320.2083477X-RAY DIFFRACTION99
8.5181-95.19980.17721480.17843456X-RAY DIFFRACTION99

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