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- PDB-1qjt: SOLUTION STRUCTURE OF THE APO EH1 DOMAIN OF MOUSE EPIDERMAL GROWT... -

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Basic information

Entry
Database: PDB / ID: 1qjt
TitleSOLUTION STRUCTURE OF THE APO EH1 DOMAIN OF MOUSE EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15, EPS15
ComponentsEPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE SUBSTRATE 15, EPS15
KeywordsGROWTH FACTOR / EH DOMAIN / EPS15 / EF-HAND / SOLUTION STRUCTURE / S100 PROTEIN
Function / homology
Function and homology information


Negative regulation of MET activity / EGFR downregulation / ubiquitin-dependent endocytosis / Golgi to endosome transport / clathrin coat of coated pit / AP-2 adaptor complex / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin-coated vesicle / ciliary membrane ...Negative regulation of MET activity / EGFR downregulation / ubiquitin-dependent endocytosis / Golgi to endosome transport / clathrin coat of coated pit / AP-2 adaptor complex / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin-coated vesicle / ciliary membrane / polyubiquitin modification-dependent protein binding / clathrin-coated pit / ubiquitin binding / SH3 domain binding / regulation of protein localization / early endosome membrane / calcium ion binding / identical protein binding / plasma membrane / cytosol
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 speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / TAD
AuthorsWhitehead, B. / Tessari, M. / Carotenuto, A. / van Bergen en Henegouwen, P.M. / Vuister, G.W.
Citation
Journal: Biochemistry / Year: 1999
Title: The Eh1 Domain of Eps15 is Structurally Classified as a Member of the S100 Subclass of EF-Hand Containing Proteins
Authors: Whitehead, B. / Tessari, M. / Carotenuto, A. / van Bergen en Henegouwen, P.M. / Vuister, G.W.
#1: Journal: J.Biomol.NMR / Year: 1998
Title: Sequence-Specific 1H, 13C and 15N Assignment of the Eh1 Domain of Mouse Eps15
Authors: Whitehead, B. / Tessari, M. / Versteeg, H.H. / van Delft, S. / van Bergen en Henegouwen, P.M. / Vuister, G.W.
History
DepositionJul 2, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.5May 15, 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 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE SUBSTRATE 15, EPS15


Theoretical massNumber of molelcules
Total (without water)10,6721
Polymers10,6721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100LOWEST OVERALL TARGET FUNCTION
RepresentativeModel #1

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Components

#1: Protein EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE SUBSTRATE 15, EPS15 / EH1


Mass: 10672.210 Da / Num. of mol.: 1 / Fragment: N-TERMINAL EH1 DOMAIN RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Details: STRUCTURED PART SELECTED FROM LARGER FRAGMENT / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K10 / References: UniProt: P42567

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111SEE J.BIOMOL.NMR 12
121465-466 (1998)
NMR detailsText: STRUCTURE DETERMINED USING TRIPLE-RESONANCE HETERONUCLEAR NMR SPECTROSCOPY

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl M / pH: 5.2 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker DRXBrukerDRX6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5P.GUNTERT, C.MUMENTHALER, K.WUTHRICHrefinement
NMRPipestructure solution
XEASYstructure solution
DYANA1.5structure solution
RefinementMethod: TAD / Software ordinal: 1
Details: STRUCTURE CALCULATION DETAILS CAN BE FOUND IN JRNL CITATION
NMR ensembleConformer selection criteria: LOWEST OVERALL TARGET FUNCTION
Conformers calculated total number: 100 / Conformers submitted total number: 30

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