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- PDB-1u39: Auto-inhibition Mechanism of X11s/Mints Family Scaffold Proteins ... -

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Basic information

Entry
Database: PDB / ID: 1u39
TitleAuto-inhibition Mechanism of X11s/Mints Family Scaffold Proteins Revealed by the Closed Conformation of the Tandem PDZ Domains
Componentsamyloid beta A4 precursor protein-binding, family A, member 1
KeywordsPROTEIN TRANSPORT / X11s/Mints / PDZ domain / scaffold protein / protein trafficking
Function / homology
Function and homology information


gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / Assembly and cell surface presentation of NMDA receptors / axo-dendritic transport / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport ...gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / Assembly and cell surface presentation of NMDA receptors / axo-dendritic transport / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport / multicellular organism growth / Schaffer collateral - CA1 synapse / synaptic vesicle / nervous system development / amyloid-beta binding / chemical synaptic transmission / regulation of gene expression / protein-containing complex assembly / in utero embryonic development / dendritic spine / cell adhesion / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / 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. / PDZ domain ...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 / torsion angle dynamics
Model type detailsminimized average
AuthorsFeng, W. / Long, J.-F. / Chan, L.-N. / He, C. / Fu, A. / Xia, J. / Ip, N.Y. / Zhang, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Autoinhibition of X11/Mint scaffold proteins revealed by the closed conformation of the PDZ tandem
Authors: Long, J.-F. / Feng, W. / Wang, R. / Chan, L.-N. / Ip, F.C. / Xia, J. / Ip, N.Y. / Zhang, M.
History
DepositionJul 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: 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

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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)8,7201
Polymers8,7201
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 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein amyloid beta A4 precursor protein-binding, family A, member 1 / X11alpha/Mint1 / phosphotyrosine-binding/-interacting domain (PTB)-bearing protein / neuronal ...X11alpha/Mint1 / phosphotyrosine-binding/-interacting domain (PTB)-bearing protein / neuronal munc18-1-interacting protein 1 / neuron-specific X11 protein / adaptor protein X11alpha


Mass: 8720.254 Da / Num. of mol.: 1 / Fragment: PDZ2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / 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
122HNCO, HN(CA)CB, CBCA(CO)NH
1333D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM uniformly 15N labelled PDZ2 in 90% H2O, 10% D2O; 100mM potassium phosphate90% H2O/10% D2O
21.0mM uniformly 15N/13C labelled PDZ2 in 90% H2O, 10% D2O; 100mM potassium phosphate90% H2O/10% D2O
31.0mM uniformly 15N/13C labelled PDZ2 in 99.9% D2O; 100mM potassium phosphate99.9% D2O
Sample conditionsIonic strength: 100mM potassium phosphate / pH: 6.5 / Pressure: 1 atm / Temperature: 303 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: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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