[English] 日本語
Yorodumi
- PDB-1f8h: STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 IN C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f8h
TitleSTRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 IN COMPLEX WITH PTGSSSTNPFR
Components
  • EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15
  • PTGSSSTNPFR
KeywordsENDOCYTOSIS/EXOCYTOSIS / COMPLEX / EH DOMAIN / NPF / CALCIUM BINDING / SIGNALING DOMAIN / EF-HAND / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


postsynaptic endocytic zone / Golgi to endosome transport / clathrin coat of coated pit / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / vesicle organization / endocytic recycling / aggresome / endosomal transport / positive regulation of receptor recycling ...postsynaptic endocytic zone / Golgi to endosome transport / clathrin coat of coated pit / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / vesicle organization / endocytic recycling / aggresome / endosomal transport / positive regulation of receptor recycling / polyubiquitin modification-dependent protein binding / clathrin-coated pit / receptor-mediated endocytosis of virus by host cell / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / EGFR downregulation / Negative regulation of MET activity / SH3 domain binding / endocytosis / protein transport / Cargo recognition for clathrin-mediated endocytosis / regulation of cell population proliferation / Clathrin-mediated endocytosis / early endosome membrane / cadherin binding / apical plasma membrane / symbiont entry into host cell / intracellular membrane-bounded organelle / calcium ion binding / glutamatergic synapse / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
EH domain / EH domain profile. / Eps15 homology domain / EH domain / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif ...EH domain / EH domain profile. / Eps15 homology domain / EH domain / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Epidermal growth factor receptor substrate 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDe Beer, T. / Hoofnagle, A.N. / Enmon, J.L. / Bowers, R.C. / Yamabhai, M. / Kay, B.K. / Overduin, M.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Molecular mechanism of NPF recognition by EH domains.
Authors: de Beer, T. / Hoofnagle, A.N. / Enmon, J.L. / Bowers, R.C. / Yamabhai, M. / Kay, B.K. / Overduin, M.
History
DepositionJun 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15
B: PTGSSSTNPFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7543
Polymers11,7132
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 5020 LOWEST NOE ENERGIES
RepresentativeModel #1lowest energy

-
Components

#1: Protein EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15 / PROTEIN EPS15


Mass: 10562.261 Da / Num. of mol.: 1 / Fragment: RESIDUES 121-218 OF HUMAN EPS15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HOMO, SAPIENS / Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / References: UniProt: P42566
#2: Protein/peptide PTGSSSTNPFR


Mass: 1151.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized peptide
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1322D NOESY
1432D NOESY
1542D NOESY
NMR detailsText: Data was collected on a 15N-labelled EH2 sample in the presence of synthetic unlabelled peptide and calcium

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride10%/90% D2O/H2O
21 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride99.999% D2O
30.2 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride10%/90% D2O/H2O
40.2 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride10%/90% D2O/H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.157ambient 298 K
20.157ambient 298 K
30.157ambient 298 K
40.157ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
NMRPipe1Delagliodata analysis
X-PLOR3.85Brungerstructure solution
X-PLOR3.85Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE R-6 SUMMATION METHOD WAS USED WITHIN A SIMULATED ANNEALING PROTOCOL.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 LOWEST NOE ENERGIES / Conformers calculated total number: 50 / Conformers submitted total number: 20

+
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