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- PDB-8ei7: Crystal structure of the WWP2 HECT domain in complex with H304, a... -

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Basic information

Entry
Database: PDB / ID: 8ei7
TitleCrystal structure of the WWP2 HECT domain in complex with H304, a Helicon Polypeptide
Components
  • H304
  • 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
DI(HYDROXYETHYL)ETHER / 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: 2.22 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: H304
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,34420
Polymers91,9603
Non-polymers1,38417
Water3,495194
1
A: NEDD4-like E3 ubiquitin-protein ligase WWP2
C: H304
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,84912
Polymers47,0352
Non-polymers81410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-38 kcal/mol
Surface area18640 Å2
MethodPISA
2
B: NEDD4-like E3 ubiquitin-protein ligase WWP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4958
Polymers44,9251
Non-polymers5707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-31 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.160, 64.300, 103.690
Angle α, β, γ (deg.)90.000, 90.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 491 through 517 or resid 519...
21(chain B and (resid 491 through 517 or resid 519...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 491 through 517 or resid 519...A491 - 517
121(chain A and (resid 491 through 517 or resid 519...A519
131(chain A and (resid 491 through 517 or resid 519...A522 - 587
141(chain A and (resid 491 through 517 or resid 519...A589 - 605
151(chain A and (resid 491 through 517 or resid 519...A607 - 718
161(chain A and (resid 491 through 517 or resid 519...A7
171(chain A and (resid 491 through 517 or resid 519...A720 - 805
181(chain A and (resid 491 through 517 or resid 519...A808 - 865
211(chain B and (resid 491 through 517 or resid 519...B491 - 517
221(chain B and (resid 491 through 517 or resid 519...B519
231(chain B and (resid 491 through 517 or resid 519...B522 - 587
241(chain B and (resid 491 through 517 or resid 519...B589 - 605
251(chain B and (resid 491 through 517 or resid 519...B607 - 718
261(chain B and (resid 491 through 517 or resid 519...B720 - 805
271(chain B and (resid 491 through 517 or resid 519...B808 - 865

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#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 H304


Mass: 2109.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 211 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


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


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M magnesium chloride, 0.1M Bis-tris pH7.5, 30% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / 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: 2.22→44.69 Å / Num. obs: 40576 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.1
Reflection shellResolution: 2.22→2.29 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3697 / CC1/2: 0.72 / % possible all: 99.8

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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: 2.22→40.12 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 2013 5.03 %
Rwork0.1999 38020 -
obs0.2031 40033 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.93 Å2 / Biso mean: 47.9493 Å2 / Biso min: 19.52 Å2
Refinement stepCycle: final / Resolution: 2.22→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 86 194 6704
Biso mean--49.71 43.11 -
Num. residues----763
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3460X-RAY DIFFRACTION14.967TORSIONAL
12B3460X-RAY DIFFRACTION14.967TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.280.36771200.27222657277798
2.28-2.340.32091770.26072701287899
2.34-2.410.32861570.25112701285899
2.41-2.480.31371160.24692733284999
2.48-2.570.35481390.23762702284199
2.57-2.680.30971500.23642683283398
2.68-2.80.28411400.21932743288399
2.8-2.940.31351630.21732687285099
2.94-3.130.27961600.21442707286799
3.13-3.370.27441340.2112703283798
3.37-3.710.23371560.18492728288499
3.71-4.240.24381540.17322725287999
4.25-5.350.22361270.16262754288198
5.35-40.120.2151200.18882796291697

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