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- PDB-1y7n: Solution structure of the second PDZ domain of the human neuronal... -

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Entry
Database: PDB / ID: 1y7n
TitleSolution structure of the second PDZ domain of the human neuronal adaptor X11alpha
ComponentsAmyloid beta A4 precursor protein-binding family A member 1
KeywordsPROTEIN TRANSPORT / copper chaperone for superoxide dismutase / neuronal adaptor
Function / homology
Function and homology information


Dopamine Neurotransmitter Release Cycle / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic modulation of chemical synaptic transmission / presynaptic active zone membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / synaptic vesicle / nervous system development ...Dopamine Neurotransmitter Release Cycle / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic modulation of chemical synaptic transmission / presynaptic active zone membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / synaptic vesicle / nervous system development / protein transport / amyloid-beta binding / protein-containing complex assembly / chemical synaptic transmission / dendritic spine / cell adhesion / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...: / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta A4 precursor protein-binding family A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics simulation, torsion angle dynamics, distance, dihedral angle restraints
AuthorsDuquesne, A.E. / de Ruijter, M. / Brouwer, J. / Drijfhout, J.W. / Nabuurs, S.B. / Spronk, C.A.E.M. / Vuister, G.W. / Ubbink, M. / Canters, G.W.
CitationJournal: J.Biomol.Nmr / Year: 2005
Title: Solution structure of the second PDZ domain of the neuronal adaptor X11alpha and its interaction with the C-terminal peptide of the human copper chaperone for superoxide dismutase
Authors: Duquesne, A.E. / de Ruijter, M. / Brouwer, J. / Drijfhout, J.W. / Nabuurs, S.B. / Spronk, C.A.E.M. / Vuister, G.W. / Ubbink, M. / Canters, G.W.
History
DepositionDec 9, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 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: Amyloid beta A4 precursor protein-binding family A member 1


Theoretical massNumber of molelcules
Total (without water)9,9341
Polymers9,9341
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Amyloid beta A4 precursor protein-binding family A member 1 / Neuron-specific X11 protein / Neuronal Munc18-1-interacting protein 1 / Mint-1 / Adapter protein X11alpha


Mass: 9933.563 Da / Num. of mol.: 1 / Fragment: second PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: APBA1 / Plasmid: pET3H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) *RP / References: UniProt: Q02410

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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 13C-separated NOESY

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Sample preparation

DetailsContents: 1.2mM PDZ2a U-15N,13C; 10mM sodium phosphate buffer; pH 6.7; 95% H2O; 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 10mM / pH: 6.7 / Pressure: 1 atm / Temperature: 290 K

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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: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2002 releaseF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
CARA1.1.8R.L.J. Kellerdata analysis
CYANA1P. Guntertstructure solution
X-PLOR2.9.6refinement
VNMRcollection
RefinementMethod: simulated annealing, molecular dynamics simulation, torsion angle dynamics, distance, dihedral angle restraints
Software ordinal: 1
Details: The final structure calculations with CYANA were started from 100 conformers with random torsion angle values. Simulated annealing with 10,000 time steps per conformer was done using the ...Details: The final structure calculations with CYANA were started from 100 conformers with random torsion angle values. Simulated annealing with 10,000 time steps per conformer was done using the DYANA torsion angle dynamics algorithm. Using the FormatConverter, developed as part of the Collaborative Computing Project for the NMR Community (CCPN), the distance and dihedral angle restraints were converted to the X-PLOR restraint format. Subsequently the 100 generated structures were refined using a sh rt restrained molecular dynamics simulation in explicit solvent in the program XPLOR-NIH. Of these, the 20 lowest energy structures were selected to form the final ensemble.
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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