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- PDB-1eh2: STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15, NMR... -

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Basic information

Entry
Database: PDB / ID: 1eh2
TitleSTRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15, NMR, 20 STRUCTURES
ComponentsEPS15
KeywordsCALCIUM BINDING / SIGNALING DOMAIN / NPF BINDING / EF-HAND / EH DOMAIN
Function / homology
Function and homology information


Golgi to endosome transport / clathrin coat of coated pit / vesicle organization / postsynaptic neurotransmitter receptor internalization / 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 / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / endocytic recycling / aggresome / endosomal transport / positive regulation of receptor recycling / polyubiquitin modification-dependent protein binding / clathrin-coated pit / 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 / Clathrin-mediated endocytosis / regulation of cell population proliferation / early endosome membrane / postsynapse / receptor-mediated endocytosis of virus by host cell / symbiont entry into host cell / cadherin binding / apical plasma membrane / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / membrane / plasma membrane / cytosol / cytoplasm
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
AuthorsDe Beer, T. / Carter, R.E. / Lobel-Rice, K.E. / Sorkin, A. / Overduin, M.
CitationJournal: Science / Year: 1998
Title: Structure and Asn-Pro-Phe binding pocket of the Eps15 homology domain.
Authors: de Beer, T. / Carter, R.E. / Lobel-Rice, K.E. / Sorkin, A. / Overduin, M.
History
DepositionJul 10, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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: EPS15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9762
Polymers11,9361
Non-polymers401
Water0
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 #1

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Components

#1: Protein EPS15 / / EH2 / EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15


Mass: 11935.817 Da / Num. of mol.: 1 / Fragment: EPS15 HOMOLOGY (EH) DOMAIN 2, RESIDUES 121-218
Source method: isolated from a genetically manipulated source
Details: THIS DOMAIN CONTAINS A CALCIUM BINDING SITE / Source: (gene. exp.) Homo sapiens (human) / Gene: EPS15 / Plasmid: PRSETA / Production host: Escherichia coli (E. coli)
Strain (production host): B834 (DE3) PLYSS AND BL21 (DE3) PLYSS
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
11115N-FILTERED TOCSY AND NOESY
12115N-1H HSQC-NOESY-HSQC
1311H-15N HMQC-J
1413D AND 4D 13C/15N-FILTERED NOESY'S
151HNCO
161CCC-TOCSY-NNH
171HCC-TOCSY-NNH
181HBCBCACONNH
191HN(CA)CB
1101(H)CCH-TOCSY
1111(HB)CB(CGCD)HD
1121(HB)CB(CGCDCE)HE
NMR detailsText: NMR EXPERIMENTS WERE PERFORMED ON UNLABELED, 15N-LABELED AND 13C,15N-LABELED EH2 PROTEIN

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Sample preparation

DetailsContents: H2O AND D2O
Sample conditionsIonic strength: 120 MILLIMOLAR / pH: 7.0 / Pressure: ATMOSPHERIC 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
Varian INOVAVarianINOVA6002

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE R-6 SUMMATION METHOD WAS USED WITHIN A SIMULATED ANNEALING PROTOCOL.
NMR ensembleConformer selection criteria: 20 LOWEST NOE ENERGIES / Conformers calculated total number: 50 / Conformers submitted total number: 20

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