[English] 日本語
Yorodumi
- PDB-6j1x: WWP1 close conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j1x
TitleWWP1 close conformation
ComponentsNEDD4-like E3 ubiquitin-protein ligase WWP1
KeywordsLIGASE / E3 ligase / close conformation / autoinhibition
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / ubiquitin ligase complex / Downregulation of ERBB4 signaling / 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 / monoatomic ion transmembrane transport ...HECT-type E3 ubiquitin transferase / ubiquitin ligase complex / Downregulation of ERBB4 signaling / 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 / monoatomic ion transmembrane transport / 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 / Protein kinase C conserved region 2 (CalB) / C2 domain / WW 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) / C2 domain / 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
NEDD4-like E3 ubiquitin-protein ligase WWP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, Z.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670730 China
National Natural Science Foundation of China31871394 China
National Natural Science Foundation of China31422015 China
CitationJournal: Nat Commun / Year: 2019
Title: A multi-lock inhibitory mechanism for fine-tuning enzyme activities of the HECT family E3 ligases.
Authors: Wang, Z. / Liu, Z. / Chen, X. / Li, J. / Yao, W. / Huang, S. / Gu, A. / Lei, Q.Y. / Mao, Y. / Wen, W.
History
DepositionDec 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / 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 / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,2573
Polymers65,0721
Non-polymers1842
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Enzyme activity assay.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-2 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.309, 45.444, 116.545
Angle α, β, γ (deg.)90.00, 93.79, 90.00
Int Tables number4
Space group name H-MP1211

-
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: 65072.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9H0M0, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris-HCl pH 7.0, 15% v/v reagent alcohol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 26023 / % possible obs: 97.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.3
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / Num. unique obs: 2599 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XMC

5xmc


Resolution: 2.3→35.81 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.04
RfactorNum. reflection% reflection
Rfree0.2705 1335 5.13 %
Rwork0.2195 --
obs0.2221 26023 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 12 54 3710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073753
X-RAY DIFFRACTIONf_angle_d0.835081
X-RAY DIFFRACTIONf_dihedral_angle_d13.7722183
X-RAY DIFFRACTIONf_chiral_restr0.049532
X-RAY DIFFRACTIONf_plane_restr0.006656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.27781330.22462466X-RAY DIFFRACTION99
2.3822-2.47760.3051350.23382451X-RAY DIFFRACTION99
2.4776-2.59030.30931230.2452479X-RAY DIFFRACTION99
2.5903-2.72680.27761400.23342458X-RAY DIFFRACTION99
2.7268-2.89760.27591470.23252380X-RAY DIFFRACTION95
2.8976-3.12120.28891480.23432473X-RAY DIFFRACTION99
3.1212-3.43510.27551500.23162466X-RAY DIFFRACTION99
3.4351-3.93160.24811080.21052518X-RAY DIFFRACTION99
3.9316-4.95130.25461220.19052461X-RAY DIFFRACTION96
4.9513-35.80980.26281290.22212536X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3228-0.276-1.60680.14480.00111.86030.0581-0.15560.00920.1106-0.106-0.0408-0.09950.14670.01910.4017-0.0924-0.0830.20410.0090.2331140.5409-58.458133.1374
21.1618-0.41270.04761.44560.54780.40150.00480.12680.02220.0351-0.06380.0609-0.2266-0.00060.05650.3698-0.0632-0.00620.2315-0.00550.206123.7548-51.412821.2894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 381 through 669 )
2X-RAY DIFFRACTION2chain 'B' and (resid 670 through 916 )

+
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