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- PDB-2jq6: Structure of EH-domain of EHD1 -

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Basic information

Entry
Database: PDB / ID: 2jq6
TitleStructure of EH-domain of EHD1
ComponentsEH domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / EH domain / EHD-1
Function / homology
Function and homology information


ciliary pocket membrane / positive regulation of endocytic recycling / positive regulation of cholesterol storage / low-density lipoprotein particle clearance / platelet dense tubular network membrane / protein localization to cilium / endocytic recycling / positive regulation of myoblast fusion / presynaptic active zone / cilium assembly ...ciliary pocket membrane / positive regulation of endocytic recycling / positive regulation of cholesterol storage / low-density lipoprotein particle clearance / platelet dense tubular network membrane / protein localization to cilium / endocytic recycling / positive regulation of myoblast fusion / presynaptic active zone / cilium assembly / endocytic vesicle / lipid droplet / cholesterol homeostasis / protein localization to plasma membrane / intracellular protein transport / cellular response to nerve growth factor stimulus / protein homooligomerization / positive regulation of neuron projection development / small GTPase binding / endocytosis / recycling endosome membrane / neuron projection development / Factors involved in megakaryocyte development and platelet production / early endosome membrane / early endosome / endosome membrane / cilium / cadherin binding / calcium ion binding / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
EH domain-containing protein, N-terminal / Domain of unknown function DUF5600 / N-terminal EH-domain containing protein / Domain of unknown function (DUF5600) / EH domain / EH domain profile. / Eps15 homology domain / EH domain / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. ...EH domain-containing protein, N-terminal / Domain of unknown function DUF5600 / N-terminal EH-domain containing protein / Domain of unknown function (DUF5600) / EH domain / EH domain profile. / Eps15 homology domain / EH domain / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKieken, F.P. / Jovic, M. / Caplan, S. / Sorgen, P.L.
CitationJournal: J.Biomol.Nmr / Year: 2007
Title: EH domain of EHD1
Authors: Kieken, F. / Jovic, M. / Naslavsky, N. / Caplan, S. / Sorgen, P.L.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0332
Polymers14,9931
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein EH domain-containing protein 1 / Testilin / hPAST1


Mass: 14992.979 Da / Num. of mol.: 1 / Fragment: EH domain, sequence database residues 401-534
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHD1, PAST, PAST1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9H4M9
#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 HN(CA)CB
1213D HN(COCA)CB
1313D HN(CO)CA
1413D HNCO
1513D HNHA
1613D 1H-15N NOESY
1713D 1H-15N TOCSY
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY
11012D 1H-15N HSQC
11112D 1H-13C HSQC

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] EH Domain of EHD-1, 3 mM CA2, 150 mM PBS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMEH Domain of EHD-1[U-99% 13C; U-99% 15N]1
3 mMCA21
150 mMPBS1
Sample conditionsIonic strength: 150 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Aria autocalibration with auto assignment. Minimization in water to prevent close contact.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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