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- PDB-2lui: Structure of the PICK PDZ domain in complex with the DAT C-terminal -

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Basic information

Entry
Database: PDB / ID: 2lui
TitleStructure of the PICK PDZ domain in complex with the DAT C-terminal
ComponentsPICK1 PDZ DOMAIN FUSED TO THE C10 DAT LIGAND
KeywordsPROTEIN BINDING / PDZ / DAT C-terminal / PICK1
Function / homology
Function and homology information


G protein-coupled glutamate receptor binding / membrane curvature sensor activity / postsynaptic endocytic zone / postsynaptic early endosome / glial cell development / cellular response to decreased oxygen levels / Arp2/3 complex binding / postsynaptic specialization / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation ...G protein-coupled glutamate receptor binding / membrane curvature sensor activity / postsynaptic endocytic zone / postsynaptic early endosome / glial cell development / cellular response to decreased oxygen levels / Arp2/3 complex binding / postsynaptic specialization / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / monoamine transport / dopamine transport / SNAP receptor activity / protein kinase C-activating G protein-coupled receptor signaling pathway / dendritic spine organization / regulation of postsynaptic neurotransmitter receptor internalization / long-term synaptic depression / dendritic spine maintenance / receptor clustering / Trafficking of GluR2-containing AMPA receptors / regulation of insulin secretion / positive regulation of receptor internalization / protein targeting / cellular response to glucose starvation / ionotropic glutamate receptor binding / cytoskeletal protein binding / ephrin receptor binding / protein kinase C binding / trans-Golgi network membrane / G protein-coupled receptor binding / phospholipid binding / intracellular protein transport / receptor tyrosine kinase binding / actin filament binding / synaptic vesicle / GTPase binding / presynaptic membrane / dendritic spine / postsynaptic density / cytoskeleton / neuron projection / protein domain specific binding / negative regulation of gene expression / signaling receptor binding / protein phosphorylation / dendrite / glutamatergic synapse / synapse / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / mitochondrion / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
PICK1, BAR domain / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / AH/BAR domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain ...PICK1, BAR domain / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / AH/BAR domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PRKCA-binding protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsErlendsson, S. / Rathje, M. / Heidarsson, P.O. / Poulsen, F.M. / Madsen, K.L. / Teilum, K. / Gether, U.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Protein interacting with C-kinase 1 (PICK1) binding promiscuity relies on unconventional PSD-95/discs-large/ZO-1 homology (PDZ) binding modes for nonclass II PDZ ligands.
Authors: Erlendsson, S. / Rathje, M. / Heidarsson, P.O. / Poulsen, F.M. / Madsen, K.L. / Teilum, K. / Gether, U.
History
DepositionJun 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Database references / Category: citation / pdbx_nmr_software / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PICK1 PDZ DOMAIN FUSED TO THE C10 DAT LIGAND


Theoretical massNumber of molelcules
Total (without water)12,4281
Polymers12,4281
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 #1closest to the average

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Components

#1: Protein PICK1 PDZ DOMAIN FUSED TO THE C10 DAT LIGAND / Protein interacting with C kinase 1 / Protein kinase C-alpha-binding protein


Mass: 12428.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pick1, Prkcabp / Plasmid: pGEX4t2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9EP80
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE C10 DAT LIGAND.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM TRIS, 125 mM sodium chloride, 2 mM DTT, 600 uM [U-100% 13C; U-100% 15N] protein, 0.25 mM DSS, 0.01 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
250 mM [U-99% 2H] TRIS, 125 mM sodium chloride, 2 mM DTT, 600 uM [U-100% 13C; U-100% 15N] protein, 0.25 mM DSS, 0.01 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMTRIS-11
125 mMsodium chloride-21
2 mMDTT-31
600 uMprotein-4[U-100% 13C; U-100% 15N]1
0.25 mMDSS-51
0.01 %sodium azide-61
50 mMTRIS-7[U-99% 2H]2
125 mMsodium chloride-82
2 mMDTT-92
600 uMprotein-10[U-100% 13C; U-100% 15N]2
0.25 mMDSS-112
0.01 %sodium azide-122
Sample conditionsIonic strength: 0.175 / pH: 7.4 / Pressure: ambient / Temperature: 288 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
VnmrJ2.2DVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
CINGGeerten W. Vuister , Alan Wilter Sousa da Silva , and Jurgen F. Doreleijersvalidation
MOLMOLKoradi, Billeter and Wuthrichrepresentation
AnalysisCCPNchemical shift assignment
AnalysisCCPNdata analysis
AnalysisCCPNpeak picking
AnalysisCCPNrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLORBrungerrestraint deposition
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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