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- PDB-1x45: Solution structure of the first PDZ domain of amyloid beta A4 pre... -

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Basic information

Entry
Database: PDB / ID: 1x45
TitleSolution structure of the first PDZ domain of amyloid beta A4 precursor protein-binding family A, member 1
Componentsamyloid beta (A4) precursor protein-binding, family A, member 1 (X11)
KeywordsENDOCYTOSIS/EXOCYTOSIS / PDZ domain / Amyloid beta A4 precursor protein-binding family A / member 1 / Neuron-specific XII protein / Adapter protein XII alpha / Neuronal Munc 18-1-interacting protein 1 Mint-1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / glutamate secretion / 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 / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / glutamate secretion / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport / Schaffer collateral - CA1 synapse / multicellular organism growth / synaptic vesicle / nervous system development / amyloid-beta binding / regulation of gene expression / protein-containing complex assembly / chemical synaptic transmission / dendritic spine / in utero embryonic development / cell adhesion / perinuclear region of cytoplasm / glutamatergic synapse / 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. ...: / 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
AuthorsQin, X.R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Solution structure of the first PDZ domain of amyloid beta A4 precursor protein-binding family A, member 1
Authors: Qin, X.R. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: amyloid beta (A4) precursor protein-binding, family A, member 1 (X11)


Theoretical massNumber of molelcules
Total (without water)9,9871
Polymers9,9871
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein amyloid beta (A4) precursor protein-binding, family A, member 1 (X11) / Neuron-specific XII protein / Neuronal Munc18-1-interacting protein 1 / Mint-1 / Adapter protein X11 alpha


Mass: 9986.510 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: APBA1, MINT1, X11 / Plasmid: P050118-02 / 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: 1.55mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.9296Kobayashi,N.data analysis
CYANA2.0.17Guntert,P.structure solution
CYANA2.0.17Guntert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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