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- PDB-1rh8: Three-dimensional structure of the calcium-free Piccolo C2A-domain -

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Basic information

Entry
Database: PDB / ID: 1rh8
TitleThree-dimensional structure of the calcium-free Piccolo C2A-domain
ComponentsPiccolo protein
KeywordsMETAL BINDING PROTEIN / beta-sandwich
Function / homology
Function and homology information


rod spherule / regulation of ubiquitin protein ligase activity / presynaptic active zone assembly / presynapse to nucleus signaling pathway / structural constituent of presynaptic active zone / cone cell pedicle / cytoskeleton of presynaptic active zone / ribbon synapse / synaptic vesicle targeting / inhibitory synapse ...rod spherule / regulation of ubiquitin protein ligase activity / presynaptic active zone assembly / presynapse to nucleus signaling pathway / structural constituent of presynaptic active zone / cone cell pedicle / cytoskeleton of presynaptic active zone / ribbon synapse / synaptic vesicle targeting / inhibitory synapse / synaptic vesicle clustering / profilin binding / presynaptic active zone cytoplasmic component / protein localization to synapse / regulation of exocytosis / calcium-dependent phospholipid binding / insulin secretion / parallel fiber to Purkinje cell synapse / Golgi-associated vesicle / presynaptic active zone / GABA-ergic synapse / transport vesicle / cytoskeleton organization / cAMP-mediated signaling / transcription corepressor binding / synapse organization / trans-Golgi network / neuromuscular junction / terminal bouton / growth cone / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / calcium ion binding / perinuclear region of cytoplasm
Similarity search - Function
Zinc finger, piccolo-type / Protein piccolo / Piccolo, FYVE-related domain 1 / Piccolo Zn-finger / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily ...Zinc finger, piccolo-type / Protein piccolo / Piccolo, FYVE-related domain 1 / Piccolo Zn-finger / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGarcia, J. / Gerber, S.H. / Sugita, S. / Sudhof, T.C. / Rizo, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: A conformational switch in the Piccolo C2A domain regulated by alternative splicing.
Authors: Garcia, J. / Gerber, S.H. / Sugita, S. / Sudhof, T.C. / Rizo, J.
History
DepositionNov 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Piccolo protein


Theoretical massNumber of molelcules
Total (without water)16,4801
Polymers16,4801
Non-polymers00
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 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Piccolo protein / / Multidomain presynaptic cytomatrix protein


Mass: 16479.602 Da / Num. of mol.: 1 / Fragment: C2A-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: PCLO / Plasmid: PGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JKS6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
132HN(CA)CB
142CBCA(CO)NH
1532D TOCSY
1632D NOESY
NMR detailsText: This structure was determined using additional triple resonance experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM Piccolo C2A-domain U-15N, 20mM acetate (pH 6.0), 150mM NaCl, 1mM EDTA, 95% H2O, 5% D2O95% H2O/5% D2O
20.8mM Piccolo C2A-domain U-15N,13C, 20mM acetate (pH 6.0), 150mM NaCl, 1mM EDTA, 95% H2O, 5% D2O95% H2O/5% D2O
30.8mM Piccolo C2A-domain U-15N, 20 mM acetate (pH 6.0), 150 mM NaCl, 1 mM EDTA, 100% D2O100% D2O
Sample conditionsIonic strength: 150mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Associatescollection
NMRPipe2.2Delaglioprocessing
NMRView4.1.2Johsondata analysis
CNS0.9Brungerstructure solution
CNS0.9Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The final structures were calculated with a total of 2316 experimental restraints, including 1994 NOE distance restraints, 116 H-bond restraints and 206 torsion angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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