[English] 日本語
Yorodumi
- PDB-2kpz: Human NEDD4 3RD WW Domain Complex with The Human T-cell Leukemia ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kpz
TitleHuman NEDD4 3RD WW Domain Complex with The Human T-cell Leukemia virus 1 GAG-Pro poliprotein Derived Peptide SDPQIPPPYVEP
Components
  • 12-mer from Gag-Pro polyprotein
  • E3 ubiquitin-protein ligase NEDD4
KeywordsLIGASE / WW DOMAIN / HTLV1 / NEDD4 / HUMAN MODULAR DOMAIN / COMPLEX / Host-virus interaction / Phosphoprotein / Ubl conjugation pathway / Aspartyl protease / Capsid protein / Lipoprotein / Metal-binding / Myristate / Protease / Viral nucleoprotein / Virion / Zinc-finger
Function / homology
Function and homology information


formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome ...formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / 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 / regulation of monoatomic ion transmembrane transport / sodium channel inhibitor activity / proline-rich region binding / RNA polymerase binding / beta-2 adrenergic receptor binding / lysosomal transport / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / neuromuscular junction development / regulation of dendrite morphogenesis / regulation of synapse organization / negative regulation of vascular endothelial growth factor receptor signaling pathway / phosphoserine residue binding / protein K63-linked ubiquitination / regulation of macroautophagy / progesterone receptor signaling pathway / ubiquitin ligase complex / Downregulation of ERBB4 signaling / Regulation of PTEN localization / regulation of membrane potential / ubiquitin binding / receptor internalization / ISG15 antiviral mechanism / Regulation of PTEN stability and activity / response to calcium ion / symbiont-mediated suppression of host gene expression / positive regulation of protein catabolic process / cellular response to UV / neuron projection development / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell cortex / ubiquitin-dependent protein catabolic process / viral nucleocapsid / nucleic acid binding / dendritic spine / aspartic-type endopeptidase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / viral translational frameshifting / protein domain specific binding / innate immune response / DNA damage response / chromatin / perinuclear region of cytoplasm / structural molecule activity / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / proteolysis / extracellular exosome / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Delta-retroviral matrix protein / Major core protein p19 / : / 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. ...Delta-retroviral matrix protein / Major core protein p19 / : / 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 / : / gag protein p24 N-terminal domain / C2 domain superfamily / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Gag-Pro polyprotein / E3 ubiquitin-protein ligase NEDD4
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 Human T-cell Leukemia virus GAP-Pro Poliprotein Derived Peptide
Authors: Iglesias-Bexiga, M. / Luque, I. / Macias, 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 Gag-Pro polyprotein


Theoretical massNumber of molelcules
Total (without water)6,9162
Polymers6,9162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area823.8 Å2
ΔGint-3.2 kcal/mol
Surface area3417.7 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 Gag-Pro polyprotein / Pr76Gag-Pro / Matrix protein p19 / MA /


Mass: 1338.460 Da / Num. of mol.: 1 / Fragment: UNP residues 113-124 / Source method: obtained synthetically / Details: chemical synthesis
Source: (synth.) Human T-cell lymphotrophic virus type 1 isolate Mel 15
References: UniProt: P0C210

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1423D CBCA(CO)NH
1523D HN(CA)CB
1623D (H)CCH-TOCSY
1713D 1H-15N NOESY
1823D 1H-13C NOESY
1913D 1H-15N TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] PROTEIN-1; 3 mM PEPTIDE-2; 20 mM sodium phosphate-3; 0.02 v/v sodium azide-4; 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] PROTEIN-5; 3 mM PEPTIDE-6; 20 mM sodium phosphate-7; 0.02 v/v sodium azide-8; 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPROTEIN-1[U-100% 15N]1
3 mMPEPTIDE-21
20 mMsodium phosphate-31
0.02 v/vsodium azide-41
1 mMPROTEIN-5[U-100% 13C; U-100% 15N]2
3 mMPEPTIDE-62
20 mMsodium phosphate-72
0.02 v/vsodium azide-82
Sample conditionspH: 7 / Pressure: ambient / Temperature: 288 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

-
Processing

NMR software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
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://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