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- PDB-5x6t: N-terminal Zinc Finger of Synaptotagmin-like Protein 4 -

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Basic information

Entry
Database: PDB / ID: 5x6t
TitleN-terminal Zinc Finger of Synaptotagmin-like Protein 4
ComponentsSynaptotagmin-like protein 4
KeywordsMETAL BINDING PROTEIN / Synaptotagmin
Function / homology
Function and homology information


regulation of plasma membrane repair / neurexin family protein binding / exocytic vesicle / platelet alpha granule membrane / multivesicular body sorting pathway / plasma membrane repair / lysosome localization / insulin secretion / transport vesicle membrane / positive regulation of exocytosis ...regulation of plasma membrane repair / neurexin family protein binding / exocytic vesicle / platelet alpha granule membrane / multivesicular body sorting pathway / plasma membrane repair / lysosome localization / insulin secretion / transport vesicle membrane / positive regulation of exocytosis / exocytosis / negative regulation of insulin secretion / positive regulation of protein secretion / intracellular protein transport / phospholipid binding / small GTPase binding / Platelet degranulation / endosome / metal ion binding / plasma membrane
Similarity search - Function
Synaptotagmin-like protein 4/5, C2A domain / Synaptotagmin-like protein 4 , FYVE-related domain / Synaptotagmin-like 1-5, C2B domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Synaptotagmin / Protein kinase C conserved region 2 (CalB) / C2 domain ...Synaptotagmin-like protein 4/5, C2A domain / Synaptotagmin-like protein 4 , FYVE-related domain / Synaptotagmin-like 1-5, C2B domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Synaptotagmin / 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
Similarity search - Domain/homology
Synaptotagmin-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K.
CitationJournal: Protein Sci. / Year: 2017
Title: The unique N-terminal zinc finger of synaptotagmin-like protein 4 reveals FYVE structure
Authors: Miyamoto, K. / Nakatani, A. / Saito, K.
History
DepositionFeb 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1723
Polymers6,0411
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: modification of Cys
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4660 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Synaptotagmin-like protein 4 / Exophilin-2 / Granuphilin


Mass: 6040.966 Da / Num. of mol.: 1 / Fragment: UNP residues 59-111 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96C24
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic1HN(CA)CO
151isotropic1HN(CO)CA
141isotropic13D HBHA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 20 mM d11 Tris-HCl, 50 mM NaCl, 1 mM d10 1,4-DL-dithiothreitol, 50 uM ZnCl2, 90% H2O/10% D2O
Label: C13 N15 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTris-HCld111
50 mMNaClnatural abundance1
1 mM1,4-DL-dithiothreitold101
50 uMZnCl2natural abundance1
Sample conditionsIonic strength: 250 mM / Label: 1 / pH: 6.9 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR softwareName: NMRView / Classification: structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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