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- SASDAB8: Protein Interacting with C-kinase 1 (PICK1) LKV, dimer contributi... -

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Basic information

Entry
Database: SASBDB / ID: SASDAB8
SampleProtein Interacting with C-kinase 1 (PICK1) LKV, dimer contribution (data decomposition).
  • PRKCA-binding protein (protein), Rattus norvegicus
Function / homology
Function and homology information


G protein-coupled glutamate receptor binding / membrane curvature sensor activity / glial cell development / postsynaptic early endosome / postsynaptic endocytic zone / Arp2/3 complex binding / cellular response to decreased oxygen levels / 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 / glial cell development / postsynaptic early endosome / postsynaptic endocytic zone / Arp2/3 complex binding / cellular response to decreased oxygen levels / postsynaptic specialization / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / SNAP receptor activity / dopamine transport / monoamine transport / dendritic spine organization / : / regulation of postsynaptic neurotransmitter receptor internalization / long-term synaptic depression / dendritic spine maintenance / receptor clustering / positive regulation of receptor internalization / Trafficking of GluR2-containing AMPA receptors / protein targeting / cellular response to glucose starvation / ionotropic glutamate receptor binding / cytoskeletal protein binding / ephrin receptor binding / regulation of insulin secretion / trans-Golgi network membrane / G protein-coupled receptor binding / protein kinase C binding / intracellular protein transport / phospholipid binding / receptor tyrosine kinase binding / actin filament binding / synaptic vesicle / GTPase binding / presynaptic membrane / dendritic spine / postsynaptic density / cytoskeleton / neuron projection / protein phosphorylation / protein domain specific binding / negative regulation of gene expression / signaling receptor binding / glutamatergic synapse / dendrite / 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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
PRKCA-binding protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
CitationJournal: Structure / Year: 2015
Title: Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering.
Authors: Morten L Karlsen / Thor S Thorsen / Niklaus Johner / Ina Ammendrup-Johnsen / Simon Erlendsson / Xinsheng Tian / Jens B Simonsen / Rasmus Høiberg-Nielsen / Nikolaj M Christensen / George ...Authors: Morten L Karlsen / Thor S Thorsen / Niklaus Johner / Ina Ammendrup-Johnsen / Simon Erlendsson / Xinsheng Tian / Jens B Simonsen / Rasmus Høiberg-Nielsen / Nikolaj M Christensen / George Khelashvili / Werner Streicher / Kaare Teilum / Bente Vestergaard / Harel Weinstein / Ulrik Gether / Lise Arleth / Kenneth L Madsen /
Abstract: PICK1 is a neuronal scaffolding protein containing a PDZ domain and an auto-inhibited BAR domain. BAR domains are membrane-sculpting protein modules generating membrane curvature and promoting ...PICK1 is a neuronal scaffolding protein containing a PDZ domain and an auto-inhibited BAR domain. BAR domains are membrane-sculpting protein modules generating membrane curvature and promoting membrane fission. Previous data suggest that BAR domains are organized in lattice-like arrangements when stabilizing membranes but little is known about structural organization of BAR domains in solution. Through a small-angle X-ray scattering (SAXS) analysis, we determine the structure of dimeric and tetrameric complexes of PICK1 in solution. SAXS and biochemical data reveal a strong propensity of PICK1 to form higher-order structures, and SAXS analysis suggests an offset, parallel mode of BAR-BAR oligomerization. Furthermore, unlike accessory domains in other BAR domain proteins, the positioning of the PDZ domains is flexible, enabling PICK1 to perform long-range, dynamic scaffolding of membrane-associated proteins. Together with functional data, these structural findings are compatible with a model in which oligomerization governs auto-inhibition of BAR domain function.
Contact author
  • Morten Karlsen (University of Copenhagen, Copenhagen, Denmark)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #318
Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 3.818116
Search similar-shape structures of this assembly by Omokage search (details)
Model #319
Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 3.818116
Search similar-shape structures of this assembly by Omokage search (details)
Model #322
Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 3.818116
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Protein Interacting with C-kinase 1 (PICK1) LKV, dimer contribution (data decomposition).
Specimen concentration: 4.20-8.80
BufferName: 50 mM Tris 125 mM NaCl 0.01 vol% reduced TX-100 / Concentration: 50.00 mM / pH: 7.4 / Composition: 125 mM NaCl, 0.01 vol% reduced TX-100
Entity #184Type: protein / Description: PRKCA-binding protein / Formula weight: 46.506 / Num. of mol.: 2 / Source: Rattus norvegicus / References: UniProt: Q9EP80
Sequence: MFADLDYDIE EDKLGIPTVP GKVTLQKDAQ NLIGISIGGG AQYCPCLYIV QVFDNTPAAL DGTVAAGDEI TGVNGRSIKG KTKVEVAKMI QEVKGEVTIH YNKLQADPKQ GMSLDIVLKK VKHRLVENMS SGTADALGLS RAILCNDGLV KRLEELERTA ELYKGMTEHT ...Sequence:
MFADLDYDIE EDKLGIPTVP GKVTLQKDAQ NLIGISIGGG AQYCPCLYIV QVFDNTPAAL DGTVAAGDEI TGVNGRSIKG KTKVEVAKMI QEVKGEVTIH YNKLQADPKQ GMSLDIVLKK VKHRLVENMS SGTADALGLS RAILCNDGLV KRLEELERTA ELYKGMTEHT KNLLRAFYEL SQTHRAFGDV FSVIGVREPQ PAASEAFVKF ADAHRSIEKF GIRLLKTIKP MLTDLNTYLN KAIPDTRLTI KKYLDVKFEY LSYCLKVKEM DDEEYSCIAL GEPLYRVSGN YEYRLILRCR QEARARFSQM RKDVLEKMEL LDQKHVQDIV FQLQRLVSTM SKYYNDCYAV LRDADVFPIE VDLAHTTLAY GPNQGGFTDG EDEEEEEEDG AAREVSKDAR GATGPTDKGG SWLKV

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Experimental information

BeamInstrument name: DORIS III X33 / City: Hamburg / : Germany / Type of source: X-ray synchrotron
DetectorName: MAR 345 Image Plate
Scan
Title: PICK1 LKV, dimer contribution (data decomposition) / Measurement date: May 11, 2015 / Cell temperature: 4 °C / Exposure time: 40 sec. / Number of frames: 4 / Unit: 1/nm /
MinMax
Q0.0675 6.2646
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 116 /
MinMax
Q0.0675 6.265
P(R) point1 116
R0 20
Result
Type of curve: merged / Standard: BSA
Comments: Structure and flexibility of PICK1 LKV mutant dimer was characterized by SAXS using data obtained by decomposing scattering from two polydisperse samples into dimer (and tetramer) ...Comments: Structure and flexibility of PICK1 LKV mutant dimer was characterized by SAXS using data obtained by decomposing scattering from two polydisperse samples into dimer (and tetramer) contributions. To obtain the dimer scattering, two samples were measured at 4.4 and 8,8 mg/ml, and decomposed as described in the reference. Models were fitted to data using a combination of rigid body modelling and EOM, based on structural components defined by NMR and MD simulations. PDB files represent structures found in the optimal ensemble. All data, in addition to that displayed for this entry, are available in the .zip archive.
ExperimentalStandardPorod
MW92 kDa92 kDa-
Volume--205 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I01.029 0.01 1.07 0.01
Radius of gyration, Rg6.03 nm0.05 6.017 nm0.91

MinMax
D-20
Guinier point13 34

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