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- PDB-1c07: STRUCTURE OF THE THIRD EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 -

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Basic information

Entry
Database: PDB / ID: 1c07
TitleSTRUCTURE OF THE THIRD EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15
ComponentsPROTEIN (EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 15)
KeywordsSIGNALING PROTEIN / CALCIUM BINDING / SIGNALING DOMAIN / NPF BINDING / FW BINDING / EF-HAND / EH DOMAIN
Function / homology
Function and homology information


Golgi to endosome transport / clathrin coat of coated pit / postsynaptic neurotransmitter receptor internalization / vesicle organization / clathrin coat assembly / endocytic recycling / aggresome / endosomal transport / positive regulation of receptor recycling / polyubiquitin modification-dependent protein binding ...Golgi to endosome transport / clathrin coat of coated pit / postsynaptic neurotransmitter receptor internalization / vesicle organization / clathrin coat assembly / endocytic recycling / aggresome / endosomal transport / positive regulation of receptor recycling / polyubiquitin modification-dependent protein binding / basal plasma membrane / clathrin-coated pit / EGFR downregulation / InlB-mediated entry of Listeria monocytogenes into host cell / Negative regulation of MET activity / SH3 domain binding / endocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein transport / early endosome membrane / regulation of cell population proliferation / postsynapse / receptor-mediated endocytosis of virus by host cell / cadherin binding / apical plasma membrane / symbiont entry into host cell / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Cytoskeletal-regulatory complex EF hand / 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 ...Cytoskeletal-regulatory complex EF hand / 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
AuthorsEnmon, J.L. / De Beer, T. / Overduin, M.
CitationJournal: Biochemistry / Year: 2000
Title: Solution structure of Eps15's third EH domain reveals coincident Phe-Trp and Asn-Pro-Phe binding sites.
Authors: Enmon, J.L. / de Beer, T. / Overduin, M.
History
DepositionJul 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 15)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6662
Polymers10,6261
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 / 50STRUCTURES WITH THE LOWEST NOE ENERGY
RepresentativeModel #8

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Components

#1: Protein PROTEIN (EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 15)


Mass: 10626.384 Da / Num. of mol.: 1 / Fragment: EPS15 HOMOLOGY (EH) DOMAIN 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P42566
#2: Chemical ChemComp-CA / CALCIUM ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
1314D 13C/15N-SEPARATED NOESY
1414D 13C-SEPARATED NOESY
151HNHA
161HMQC-J
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 0.5-1MM EH3; 20MM D-TRIS, 100MM KCL, 2MM CACL2, 2MM NAN3, 0.1MM D-DTT; 95% H2O, 5% D2O
Sample conditionsIonic strength: 100mM KCL, 2mM CACL2, 2mM NAN3 / pH: 7.8 / Pressure: AMBIENT / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionClassification
X-PLOR3.84structure solution
X-PLOR3.84refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LOWEST NOE ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 20

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