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- PDB-8ei8: Crystal structure of the WWP2 HECT domain in complex with H308, a... -

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Basic information

Entry
Database: PDB / ID: 8ei8
TitleCrystal structure of the WWP2 HECT domain in complex with H308, a Helicon Polypeptide
Components
  • H308
  • NEDD4-like E3 ubiquitin-protein ligase WWP2
KeywordsLIGASE / E3 ligase / complex / stapled peptide
Function / homology
Function and homology information


negative regulation of transporter activity / negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / transcription factor binding / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle ...negative regulation of transporter activity / negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / transcription factor binding / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / protein K63-linked ubiquitination / negative regulation of Notch signaling pathway / ubiquitin ligase complex / protein autoubiquitination / regulation of membrane potential / negative regulation of DNA-binding transcription factor activity / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein modification process / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / RNA polymerase II-specific DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / protein ubiquitination / symbiont entry into host cell / negative regulation of gene expression / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
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 / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. ...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) / 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
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / N,N'-(1,4-phenylene)diacetamide / NEDD4-like E3 ubiquitin-protein ligase WWP2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, K. / Tokareva, O.S. / Thomson, T.M. / Verdine, G.L. / McGee, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2023
Title: Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides.
Authors: Tokareva, O.S. / Li, K. / Travaline, T.L. / Thomson, T.M. / Swiecicki, J.M. / Moussa, M. / Ramirez, J.D. / Litchman, S. / Verdine, G.L. / McGee, J.H.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEDD4-like E3 ubiquitin-protein ligase WWP2
B: H308
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7228
Polymers46,9992
Non-polymers7236
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-1 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.380, 117.810, 65.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein NEDD4-like E3 ubiquitin-protein ligase WWP2 / Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain- ...Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain-containing protein 2


Mass: 44925.391 Da / Num. of mol.: 1 / Fragment: HECT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP2 / Production host: Escherichia coli (E. coli)
References: UniProt: O00308, HECT-type E3 ubiquitin transferase
#2: Protein/peptide H308


Mass: 2073.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 6 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Magnesium Chloride, 0.1M Bis-Tris pH 6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→43.77 Å / Num. obs: 9862 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.248 / Net I/σ(I): 8
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1564 / CC1/2: 0.814 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y07

4y07


Resolution: 2.9→43.77 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3067 486 4.93 %
Rwork0.2366 9372 -
obs0.2399 9858 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.28 Å2 / Biso mean: 61.1609 Å2 / Biso min: 27.45 Å2
Refinement stepCycle: final / Resolution: 2.9→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 49 0 3344
Biso mean--68.01 --
Num. residues----391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9-3.320.38261920.283830203212
3.32-4.180.34191420.23731233265
4.18-43.770.25751520.221932293381
Refinement TLS params.Method: refined / Origin x: -22.7921 Å / Origin y: -26.6122 Å / Origin z: 10.9467 Å
111213212223313233
T0.2386 Å20.0159 Å20.0104 Å2-0.2436 Å20.026 Å2--0.2493 Å2
L0.4465 °2-0.2424 °20.1175 °2-0.5689 °2-0.0984 °2--1.1175 °2
S0.0401 Å °-0.0595 Å °0.0025 Å °0.0368 Å °-0.0292 Å °-0.0509 Å °0.0037 Å °0.034 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA492 - 865
2X-RAY DIFFRACTION1allB1 - 17
3X-RAY DIFFRACTION1allB101
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1 - 3
6X-RAY DIFFRACTION1allF1

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