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

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Basic information

Entry
Database: PDB / ID: 5hpk
TitleSystem-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: NEDD4L and UbV NL.1
Components
  • E3 ubiquitin-protein ligase NEDD4-like
  • Ubiquitin variant NL.1
KeywordsLIGASE / HECT / E3 ligase / NEDD4L / ubiquitin / Ubv
Function / homology
Function and homology information


positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of sodium ion import across plasma membrane / negative regulation of potassium ion export across plasma membrane / negative regulation of potassium ion transmembrane transport / negative regulation of protein localization to cell surface / positive regulation of dendrite extension / regulation of membrane repolarization / regulation of membrane depolarization ...positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of sodium ion import across plasma membrane / negative regulation of potassium ion export across plasma membrane / negative regulation of potassium ion transmembrane transport / negative regulation of protein localization to cell surface / positive regulation of dendrite extension / regulation of membrane repolarization / regulation of membrane depolarization / receptor catabolic process / regulation of sodium ion transmembrane transport / potassium channel inhibitor activity / ventricular cardiac muscle cell action potential / response to insecticide / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / regulation of dendrite morphogenesis / neuromuscular junction development / regulation of synapse organization / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / sodium channel regulator activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein monoubiquitination / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein K48-linked ubiquitination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / multivesicular body / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / cytosolic ribosome / 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 / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / 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 / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins
Similarity search - Function
Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / 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, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / 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 / C2 domain / C2 domain profile. / WW/rsp5/WWP domain signature. / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eL40 fusion protein / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.431 Å
AuthorsWu, K.-P. / Mukherjee, M. / Mercredi, P.Y. / Schulman, B.A.
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, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase NEDD4-like
B: Ubiquitin variant NL.1


Theoretical massNumber of molelcules
Total (without water)55,3022
Polymers55,3022
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-13 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.306, 151.306, 85.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1039-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase NEDD4-like / NEDD4.2 / Nedd4-2


Mass: 45251.492 Da / Num. of mol.: 1 / Fragment: HECT domain (UNP residues 594-975)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96PU5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Ubiquitin variant NL.1


Mass: 10050.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSF-duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62987*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 4.45 Å3/Da / Density % sol: 72.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Sodium cacodylate, NaCl, PEG 8000, 1-butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.431→45.976 Å / Num. obs: 38009 / % possible obs: 99.79 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 17.36
Reflection shellResolution: 2.431→2.4919 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.56 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ND7

1nd7


Resolution: 2.431→35.663 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.05
RfactorNum. reflection% reflection
Rfree0.2268 1931 5.08 %
Rwork0.2114 --
obs0.2122 37983 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.431→35.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 0 131 3876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113841
X-RAY DIFFRACTIONf_angle_d1.2075186
X-RAY DIFFRACTIONf_dihedral_angle_d15.171456
X-RAY DIFFRACTIONf_chiral_restr0.052543
X-RAY DIFFRACTIONf_plane_restr0.006674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4311-2.49190.30841270.26952539X-RAY DIFFRACTION100
2.4919-2.55920.3011280.25422553X-RAY DIFFRACTION100
2.5592-2.63450.28281240.24932532X-RAY DIFFRACTION100
2.6345-2.71950.28191490.24532531X-RAY DIFFRACTION100
2.7195-2.81670.30431430.25112551X-RAY DIFFRACTION100
2.8167-2.92940.26881350.24272533X-RAY DIFFRACTION100
2.9294-3.06270.31861340.24632566X-RAY DIFFRACTION100
3.0627-3.22410.24131420.2332557X-RAY DIFFRACTION100
3.2241-3.42590.27031350.23442575X-RAY DIFFRACTION100
3.4259-3.69020.2661210.21522582X-RAY DIFFRACTION100
3.6902-4.06110.22291290.20382598X-RAY DIFFRACTION100
4.0611-4.64760.20381550.17922588X-RAY DIFFRACTION100
4.6476-5.85130.17141390.18932645X-RAY DIFFRACTION100
5.8513-35.6670.1781700.18952702X-RAY DIFFRACTION98

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