[English] 日本語
Yorodumi
- PDB-8ei7: Crystal structure of the WWP2 HECT domain in complex with H304, a... -

+
Open data


ID or keywords:

Loading...

-
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 transporter activity / negative regulation of protein transport / extracellular transport / negative regulation of potassium ion export across plasma membrane / potassium channel inhibitor activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / transcription factor binding / RHOJ GTPase cycle / RHOQ GTPase cycle ...negative regulation of transporter activity / negative regulation of protein transport / extracellular transport / negative regulation of potassium ion export across plasma membrane / potassium channel inhibitor 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 Notch signaling pathway / protein K63-linked ubiquitination / ubiquitin ligase complex / transcription regulator inhibitor activity / protein autoubiquitination / regulation of membrane potential / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein ubiquitination / negative regulation of gene expression / negative regulation of DNA-templated transcription / symbiont entry into host cell / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / membrane / cytoplasm / cytosol
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 / 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 / C2 domain / WW/rsp5/WWP domain signature. / 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
Non-polymers , 7 types, 211 molecules

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


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


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


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


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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more