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- PDB-2k3h: Structural determinants for Ca2+ and PIP2 binding by the C2A doma... -

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Basic information

Entry
Database: PDB / ID: 2k3h
TitleStructural determinants for Ca2+ and PIP2 binding by the C2A domain of rabphilin-3A
ComponentsRabphilin-3A
KeywordsPROTEIN TRANSPORT / PIP2 / C2 domain / Calcium / TAMA mechanism / Cell junction / Metal-binding / Phosphoprotein / Synapse / Transport / Zinc / Zinc-finger
Function / homology
Function and homology information


selenium binding / spontaneous neurotransmitter secretion / regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / extrinsic component of membrane / synaptic vesicle priming ...selenium binding / spontaneous neurotransmitter secretion / regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / extrinsic component of membrane / synaptic vesicle priming / phosphate ion binding / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / intracellular protein transport / neuromuscular junction / small GTPase binding / synaptic vesicle membrane / synaptic vesicle / postsynaptic membrane / dendritic spine / neuron projection / calcium ion binding / synapse / protein-containing complex binding / protein-containing complex / zinc ion binding / cytosol
Similarity search - Function
Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin ...Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsCa2+ bound form of the C2A domain of Rabphilin-3A
AuthorsCoudevylle, N. / Montaville, P. / Leonov, A. / Zweckstetter, M. / Becker, S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Determinants for Ca2+ and Phosphatidylinositol 4,5-Bisphosphate Binding by the C2A Domain of Rabphilin-3A.
Authors: Coudevylle, N. / Montaville, P. / Leonov, A. / Zweckstetter, M. / Becker, S.
History
DepositionMay 8, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 1.3May 29, 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: Rabphilin-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1533
Polymers16,0731
Non-polymers802
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Rabphilin-3A / C2 domain


Mass: 16073.175 Da / Num. of mol.: 1 / Fragment: C2A domain (UNP residues 368-570)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rph3a / Production host: Escherichia coli (E. coli) / References: UniProt: P47708
#2: Chemical ChemComp-CA / CALCIUM ION / CALCIUM (II) ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Ca2+ bound form of the C2A domain of Rabphilin-3A
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] C2A domain, 20 mM Na acetate, 150 mM NaCl, 20 mM CaCl2, 1 mM DTT, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC2A domain[U-13C; U-15N]1
20 mMNa acetate1
150 mMNaCl1
20 mMCaCl21
1 mMDTT1
Sample conditionsIonic strength: 150 / pH: 5 / Temperature: 301 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameDeveloperClassification
CARARochus Kellerchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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