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- PDB-8ei6: Crystal structure of the WWP2 HECT domain in complex with H305, a... -

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Basic information

Entry
Database: PDB / ID: 8ei6
TitleCrystal structure of the WWP2 HECT domain in complex with H305, a Helicon Polypeptide
Components
  • H305
  • NEDD4-like E3 ubiquitin-protein ligase WWP2
KeywordsLIGASE / E3 ligase / complex / stapled peptide
Function / homology
Function and homology information


negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / negative regulation of transporter activity / regulation of monoatomic ion transmembrane transport / negative regulation of Notch signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / protein K63-linked ubiquitination ...negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / negative regulation of transporter activity / regulation of monoatomic ion transmembrane transport / negative regulation of Notch signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / protein K63-linked ubiquitination / RHOU GTPase cycle / transcription factor binding / protein autoubiquitination / ubiquitin ligase complex / regulation of membrane potential / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein modification process / negative regulation of DNA-binding transcription factor activity / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / membrane / nucleus / 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. / C2 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) / 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 WWP2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 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

Downloads & links

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Assembly

Deposited unit
A: NEDD4-like E3 ubiquitin-protein ligase WWP2
B: NEDD4-like E3 ubiquitin-protein ligase WWP2
C: H305
D: H305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9546
Polymers93,5694
Non-polymers3842
Water0
1
A: NEDD4-like E3 ubiquitin-protein ligase WWP2
C: H305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9773
Polymers46,7852
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-13 kcal/mol
Surface area19780 Å2
MethodPISA
2
B: NEDD4-like E3 ubiquitin-protein ligase WWP2
D: H305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9773
Polymers46,7852
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-11 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.620, 71.320, 211.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 492 through 615 or resid 617 through 725 or resid 727 through 865))
21(chain B and (resid 492 through 615 or resid 617 through 725 or resid 727 through 865))
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPALAALA(chain A and (resid 492 through 615 or resid 617 through 725 or resid 727 through 865))AA492 - 6153 - 126
121TYRTYRLEULEU(chain A and (resid 492 through 615 or resid 617 through 725 or resid 727 through 865))AA617 - 725128 - 236
131GLYGLYGLUGLU(chain A and (resid 492 through 615 or resid 617 through 725 or resid 727 through 865))AA727 - 865238 - 376
211ASPASPALAALA(chain B and (resid 492 through 615 or resid 617 through 725 or resid 727 through 865))BB492 - 6153 - 126
221TYRTYRLEULEU(chain B and (resid 492 through 615 or resid 617 through 725 or resid 727 through 865))BB617 - 725128 - 236
231GLYGLYGLUGLU(chain B and (resid 492 through 615 or resid 617 through 725 or resid 727 through 865))BB727 - 865238 - 376
112PROPROPHEPHEchain CCC2 - 173 - 18
212PROPROPHEPHEchain DDD2 - 173 - 18

NCS ensembles :
ID
1
2

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Components

#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.: 2 / 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 H305


Mass: 1859.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O2
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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% w/v PEG 8000, 0.1M MES Sodium Salt pH6.5, 0.2M Ammonium Sulfate, 4% v/v 1,3-Propanediol

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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: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→49.07 Å / Num. obs: 12498 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.19 / Net I/σ(I): 10.2
Reflection shellResolution: 3.6→3.94 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2921 / CC1/2: 0.979 / % possible all: 99.9

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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: 3.62→49.07 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 957 10.17 %
Rwork0.2592 8457 -
obs0.2614 9414 76.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.37 Å2 / Biso mean: 78.8667 Å2 / Biso min: 4.39 Å2
Refinement stepCycle: final / Resolution: 3.62→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6432 0 28 0 6460
Biso mean--92.73 --
Num. residues----766
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2214X-RAY DIFFRACTION6.877TORSIONAL
12B2214X-RAY DIFFRACTION6.877TORSIONAL
21C88X-RAY DIFFRACTION6.877TORSIONAL
22D88X-RAY DIFFRACTION6.877TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.62-3.810.2858220.342417519712
3.81-4.050.2962700.312357464438
4.05-4.360.321470.27521315146286
4.36-4.80.26861810.234315601741100
4.8-5.50.26391710.24615711742100
5.5-6.920.29551750.269315881763100
6.92-49.070.24981910.238516741865100

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