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- PDB-3rpb: THE C2B-DOMAIN OF RABPHILIN: STRUCTURAL VARIATIONS IN A JANUS-FAC... -

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Basic information

Entry
Database: PDB / ID: 3rpb
TitleTHE C2B-DOMAIN OF RABPHILIN: STRUCTURAL VARIATIONS IN A JANUS-FACED DOMAIN
ComponentsRABPHILIN 3-A
KeywordsENDOCYTOSIS/EXOCYTOSIS / C2-DOMAINS / C2B-DOMAIN / RABPHILIN / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / synaptic vesicle priming ...selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / synaptic vesicle priming / extrinsic component of membrane / exocytosis / phosphate ion binding / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / intracellular protein transport / neuromuscular junction / phospholipid binding / synaptic vesicle membrane / small GTPase binding / synaptic vesicle / postsynaptic membrane / dendritic spine / neuron projection / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / zinc ion binding
Similarity search - Function
Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin ...Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / TORSION ANGLE SIMULATED ANNEALING
AuthorsUbach, J. / Garcia, J. / Nittler, M.P. / Sudhof, T.C. / Rizo, J.
CitationJournal: Nat.Cell Biol. / Year: 1999
Title: Structure of the Janus-faced C2B domain of rabphilin.
Authors: Ubach, J. / Garcia, J. / Nittler, M.P. / Sudhof, T.C. / Rizo, J.
History
DepositionApr 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 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: RABPHILIN 3-A


Theoretical massNumber of molelcules
Total (without water)16,2541
Polymers16,2541
Non-polymers00
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 / -LOWEST OVERALL ENERGY
Representative

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Components

#1: Protein RABPHILIN 3-A


Mass: 16253.784 Da / Num. of mol.: 1 / Fragment: C2B DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P47709

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 95% WATER/5% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.1 / Temperature: 304.5 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: TORSION ANGLE SIMULATED ANNEALING / Software ordinal: 1 / Details: TORSION ANGLE SIMULATED ANNEALING
NMR ensembleConformer selection criteria: LOWEST OVERALL ENERGY / Conformers submitted total number: 20

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