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- PDB-8ei4: Crystal structure of the WWP1 HECT domain in complex with H302, a... -

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Basic information

Entry
Database: PDB / ID: 8ei4
TitleCrystal structure of the WWP1 HECT domain in complex with H302, a Helicon Polypeptide
Components
  • H302
  • NEDD4-like E3 ubiquitin-protein ligase WWP1
KeywordsLIGASE / E3 ligase / complex / stapled peptide
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / ubiquitin ligase complex / Downregulation of ERBB4 signaling / monoatomic ion transmembrane transport / central nervous system development / Stimuli-sensing channels / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation ...HECT-type E3 ubiquitin transferase / ubiquitin ligase complex / Downregulation of ERBB4 signaling / monoatomic ion transmembrane transport / central nervous system development / Stimuli-sensing channels / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / symbiont entry into host cell / negative regulation of DNA-templated transcription / signal transduction / extracellular exosome / nucleus / plasma 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 / C2 domain / 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 / 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
Similarity search - Domain/homology
N,N'-(1,4-phenylene)diacetamide / NEDD4-like E3 ubiquitin-protein ligase WWP1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEDD4-like E3 ubiquitin-protein ligase WWP1
B: H302
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7677
Polymers46,3262
Non-polymers4405
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-5 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.420, 51.210, 58.640
Angle α, β, γ (deg.)112.090, 99.610, 102.510
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NEDD4-like E3 ubiquitin-protein ligase WWP1 / Atrophin-1-interacting protein 5 / AIP5 / HECT-type E3 ubiquitin transferase WWP1 / TGIF- ...Atrophin-1-interacting protein 5 / AIP5 / HECT-type E3 ubiquitin transferase WWP1 / TGIF-interacting ubiquitin ligase 1 / Tiul1 / WW domain-containing protein 1


Mass: 44430.895 Da / Num. of mol.: 1 / Fragment: HECT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H0M0, HECT-type E3 ubiquitin transferase
#2: Protein/peptide H302


Mass: 1895.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Sodium acetate, 0.1 M Sodium citrate pH 5.5, 5% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.181 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 2.43→45.18 Å / Num. obs: 16258 / % possible obs: 94 % / Redundancy: 2.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.3
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1472 / CC1/2: 0.872 / % possible all: 80.3

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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: 6J1X

6j1x


Resolution: 2.43→45.18 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 33.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2808 785 5.09 %
Rwork0.2192 14646 -
obs0.2223 15431 89.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.15 Å2 / Biso mean: 45.5991 Å2 / Biso min: 18.53 Å2
Refinement stepCycle: final / Resolution: 2.43→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 30 35 3210
Biso mean--56.1 44.83 -
Num. residues----381
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.580.41741050.31622219232481
2.58-2.780.33771380.2662510264891
2.78-3.060.32291320.24312485261791
3.06-3.50.33631360.23492455259190
3.51-4.410.24921270.19582485261291
4.41-45.180.2331470.192492263991

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