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- PDB-1fi6: SOLUTION STRUCTURE OF THE REPS1 EH DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1fi6
TitleSOLUTION STRUCTURE OF THE REPS1 EH DOMAIN
ComponentsEH DOMAIN PROTEIN REPS1EF hand
Keywordsendocytosis/exocytosis / EPS15 HOMOLOGY DOMAIN / EF HAND / CALCIUM / RAS SIGNAL TRANSDUCTION / endocytosis-exocytosis COMPLEX
Function / homology
Function and homology information


Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / endosomal transport / clathrin-coated pit / receptor-mediated endocytosis / SH3 domain binding / endocytosis / calcium ion binding / plasma membrane
Similarity search - Function
RalBP1-associated Eps domain-containing protein 1 / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...RalBP1-associated Eps domain-containing protein 1 / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RalBP1-associated Eps domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsKim, S. / Baleja, J.D.
Citation
Journal: Biochemistry / Year: 2001
Title: Solution structure of the Reps1 EH domain and characterization of its binding to NPF target sequences.
Authors: Kim, S. / Cullis, D.N. / Feig, L.A. / Baleja, J.D.
#1: Journal: Thesis / Year: 2000
Title: Chapter 3: Studies of Protein Structure and Interaction using Nuclear Magnetic Resonance Spectroscopy:Applications to the Reps1 EH Domain and MicrocinB17 Propeptide
Authors: Kim, S.
History
DepositionAug 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _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: EH DOMAIN PROTEIN REPS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6872
Polymers10,6471
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)30 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein EH DOMAIN PROTEIN REPS1 / EF hand


Mass: 10647.128 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: O54916
#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 13C-separated NOESY
1223D 15N-separated NOESY
1332D NOESY
143DQF-COSY
NMR detailsText: The structure was determined using heteronuclear 2D and 3D NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Reps1 EH domain U-15N,13C; 10mM d-imidazole buffer, 1.5mM CaCl2; 90% H2O, 10% D2O90% H2O/10% D2O
21mM Reps1 EH domain U-15N; 10mM d-imidazole buffer, 1.5mM CaCl2; 90% H2O, 10% D2O90% H2O/10% D2O
31mM Reps1 EH domain; 10mM d-imidazole buffer, 1.5mM CaCl299% D2O
Sample conditionsIonic strength: 10mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 30 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.7Brukercollection
XwinNMR1.7Brukerprocessing
Felix1.1.2Hare/Biosymdata analysis
X-PLOR3.1Brunger/Biosymstructure solution
X-PLOR3.1Brunger/Biosymrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1265 restraints, 1143 are NOE-derived distance constraints, 122 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 30

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