[English] 日本語
Yorodumi
- PDB-2kq0: Human NEDD4 3rd WW Domain Complex with Ebola Zaire Virus Matrix P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kq0
TitleHuman NEDD4 3rd WW Domain Complex with Ebola Zaire Virus Matrix Protein VP40 Derived Peptide ILPTAPPEYMEA
Components
  • 12-mer from Matrix protein VP40
  • E3 ubiquitin-protein ligase NEDD4
KeywordsLIGASE / WW DOMAIN / COMPLEX / VIRUS L DOMAIN / NEDD4 / EBOLA / Host-virus interaction / Phosphoprotein / Ubl conjugation pathway / Cell membrane / Ribonucleoprotein / RNA replication / RNA-binding / Viral matrix protein / Virion
Function / homology
Function and homology information


formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway ...formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / host cell late endosome membrane / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome / apicolateral plasma membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / proline-rich region binding / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / lysosomal transport / neuromuscular junction development / regulation of dendrite morphogenesis / regulation of synapse organization / negative regulation of vascular endothelial growth factor receptor signaling pathway / viral budding via host ESCRT complex / progesterone receptor signaling pathway / protein K63-linked ubiquitination / host cell membrane / phosphoserine residue binding / regulation of macroautophagy / beta-2 adrenergic receptor binding / ubiquitin ligase complex / Downregulation of ERBB4 signaling / Regulation of PTEN localization / viral budding from plasma membrane / ubiquitin binding / regulation of membrane potential / receptor internalization / ISG15 antiviral mechanism / Regulation of PTEN stability and activity / response to calcium ion / positive regulation of protein catabolic process / cellular response to UV / neuron projection development / ubiquitin protein ligase activity / host cell / Antigen processing: Ubiquitination & Proteasome degradation / cell cortex / ubiquitin-dependent protein catabolic process / structural constituent of virion / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / ribonucleoprotein complex / membrane raft / protein domain specific binding / innate immune response / virus-mediated perturbation of host defense response / DNA damage response / chromatin / host cell plasma membrane / virion membrane / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40 / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with ...EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40 / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase NEDD4 / Matrix protein VP40
Similarity search - Component
Biological speciesHomo sapiens (human)
Human T-cell lymphotrophic virus type 1 isolate Mel 15
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsIglesias-Bexiga, M. / Macias, M. / Bonet, R. / Blanco, F.J. / Cobos, E.S. / Luque, I.
CitationJournal: To be Published
Title: Human NEDD4 3rd WW Domain Complex with Ebola Zaire Virus Matrix Protein VP40 Derived Peptide
Authors: Iglesias-Bexiga, M.
History
DepositionOct 23, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase NEDD4
B: 12-mer from Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)6,9092
Polymers6,9092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area764.5 Å2
ΔGint-4.3 kcal/mol
Surface area3556.1 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4 / Neural precursor cell expressed developmentally down-regulated protein 4 / NEDD-4 / Cell ...Neural precursor cell expressed developmentally down-regulated protein 4 / NEDD-4 / Cell proliferation-inducing gene 53 protein


Mass: 5577.272 Da / Num. of mol.: 1 / Fragment: 3rd WW Domain, UNP residues 834-878
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21(DE3)
References: UniProt: P46934, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide 12-mer from Matrix protein VP40 / Membrane-associated protein VP40


Mass: 1331.532 Da / Num. of mol.: 1 / Fragment: UNP residues 5-16 / Source method: obtained synthetically / Details: chemical synthesis
Source: (synth.) Human T-cell lymphotrophic virus type 1 isolate Mel 15
References: UniProt: Q05128

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

-
Sample preparation

DetailsContents: 1mM [U-100% 15N] PROTEIN; 10mM PEPTIDE; 20mM sodium phosphate; 0.02 v/v % sodium azide; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPROTEIN-1[U-100% 15N]1
10 mMPEPTIDE-21
20 mMsodium phosphate-31
0.02 v/vsodium azide-41
Sample conditionspH: 7.00 / Pressure: ambient / Temperature: 288 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospinprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20 / Representative conformer: 1

+
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://pdbjlvh1.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