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- PDB-2kff: Structure of the C-terminal domain of EHD1 with FNYESTNPFTAK -

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Basic information

Entry
Database: PDB / ID: 2kff
TitleStructure of the C-terminal domain of EHD1 with FNYESTNPFTAK
Components
  • EH domain-containing protein 1
  • Rab11-FIP2 NPF peptide FNYESTNPFTAK
KeywordsPROTEIN BINDING / EHD1 / Calcium / Cell membrane / Coiled coil / Endosome / Membrane / Nucleotide-binding / Phosphoprotein
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 / endocytic vesicle ...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 / endocytic vesicle / cilium assembly / 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 / recycling endosome membrane / endocytosis / 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
Model detailslowest energy, model 10
AuthorsKieken, F. / Jovic, M. / Tonelli, M. / Naslavsky, N. / Caplan, S. / Sorgen, P.
CitationJournal: Protein Sci. / Year: 2009
Title: Structural insight into the interaction of proteins containing NPF, DPF, and GPF motifs with the C-terminal EH-domain of EHD1.
Authors: Kieken, F. / Jovic, M. / Tonelli, M. / Naslavsky, N. / Caplan, S. / Sorgen, P.L.
History
DepositionFeb 20, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EH domain-containing protein 1
B: Rab11-FIP2 NPF peptide FNYESTNPFTAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1143
Polymers13,0742
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)10 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11654.334 Da / Num. of mol.: 1 / Fragment: EH domain, residues 435-534
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHD1, PAST, PAST1, CDABP0131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H4M9
#2: Protein/peptide Rab11-FIP2 NPF peptide FNYESTNPFTAK


Mass: 1419.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide has been synthesized chemically
#3: 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1612D 13CFiltered-13CfilteredNOESY
1712D 13C-filtered-13C editedNOESY
1812D 13C-filtered-15N editedNOESY
1912D 15N filtered NOESY

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Sample preparation

DetailsContents: 0.6 mM [U-99% 13C; U-99% 15N] EH domain of EHD1, 3 mM Rab11-FIP2 NPF peptide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMEH domain of EHD1[U-99% 13C; U-99% 15N]1
3 mMRab11-FIP2 NPF peptide1
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ProcheckNMRLaskowski and MacArthurdata analysis
VNMRVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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