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- PDB-2mho: Solution State Structure PSD-95 PDZ1 with 5HT2C Receptor peptide -

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Basic information

Entry
Database: PDB / ID: 2mho
TitleSolution State Structure PSD-95 PDZ1 with 5HT2C Receptor peptide
Components
  • Disks large homolog 4
  • peptide from 5-hydroxytryptamine receptor 2C
KeywordsPROTEIN BINDING / PDZ / 5-hydroxytryptamine receptor fragment / PSD-95
Function / homology
Function and homology information


Serotonin receptors / regulation of corticotropin-releasing hormone secretion / phospholipase D-activating G protein-coupled receptor signaling pathway / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / regulation of appetite / neuronal ion channel clustering / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / P2Y1 nucleotide receptor binding / Gq/11-coupled serotonin receptor activity ...Serotonin receptors / regulation of corticotropin-releasing hormone secretion / phospholipase D-activating G protein-coupled receptor signaling pathway / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / regulation of appetite / neuronal ion channel clustering / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / P2Y1 nucleotide receptor binding / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / beta-1 adrenergic receptor binding / G protein-coupled serotonin receptor complex / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / regulation of nervous system process / synaptic vesicle maturation / positive regulation of neuron projection arborization / positive regulation of acetylcholine secretion, neurotransmission / regulation of grooming behavior / positive regulation of gamma-aminobutyric acid secretion / receptor localization to synapse / serotonin receptor activity / negative regulation of dopamine metabolic process / G protein-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / vocalization behavior / serotonin receptor signaling pathway / cerebellar mossy fiber / LGI-ADAM interactions / proximal dendrite / sensitization / neuron spine / Trafficking of AMPA receptors / protein localization to synapse / neurotransmitter receptor activity / behavioral response to nicotine / AMPA glutamate receptor clustering / cellular response to potassium ion / Activation of Ca-permeable Kainate Receptor / dendritic branch / positive regulation of dendrite morphogenesis / serotonin binding / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / frizzled binding / acetylcholine receptor binding / neuron projection terminus / dendritic spine organization / regulation of NMDA receptor activity / feeding behavior / positive regulation of synapse assembly / Synaptic adhesion-like molecules / G alpha (q) signalling events / NMDA selective glutamate receptor signaling pathway / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / cGMP-mediated signaling / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / social behavior / locomotory exploration behavior / AMPA glutamate receptor complex / regulation of neuronal synaptic plasticity / neuromuscular process controlling balance / kinesin binding / excitatory synapse / positive regulation of excitatory postsynaptic potential / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of fat cell differentiation / behavioral fear response / positive regulation of synaptic transmission / glutamate receptor binding / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / animal organ regeneration / ionotropic glutamate receptor binding / positive regulation of vasoconstriction / release of sequestered calcium ion into cytosol / dendrite cytoplasm / positive regulation of calcium-mediated signaling / cell periphery / PDZ domain binding / locomotory behavior / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / neuromuscular junction / cerebral cortex development / cell-cell adhesion / kinase binding / intracellular calcium ion homeostasis / cell junction / synaptic vesicle / cell-cell junction
Similarity search - Function
5-Hydroxytryptamine 2C receptor / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / 5-hydroxytryptamine receptor family / : / Guanylate kinase, conserved site ...5-Hydroxytryptamine 2C receptor / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / 5-hydroxytryptamine receptor family / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / Serpentine type 7TM GPCR chemoreceptor Srsx / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
5-hydroxytryptamine receptor 2C / Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, simulated annealing
Model detailsclosest to the average, model5
AuthorsDorr, L.A. / Phelan, M.M. / Lian, L.
CitationJournal: To be Published
Title: Interactions of the 5-Hydroxytryptamine Receptor 2a and 2c Variants with the PSD-MAGUK proteins, PSD-95 and SAP997
Authors: Dorr, L.A. / Phelan, M.M. / Lian, L.
History
DepositionNov 29, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large homolog 4
B: peptide from 5-hydroxytryptamine receptor 2C


Theoretical massNumber of molelcules
Total (without water)11,5982
Polymers11,5982
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 #1closest to the average

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Components

#1: Protein Disks large homolog 4 / Postsynaptic density protein 95 / PSD-95 / Synapse-associated protein 90 / SAP-90 / SAP90


Mass: 10621.968 Da / Num. of mol.: 1 / Fragment: PDZ 1, UNP residues 60-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Production host: Escherichia coli (E. coli) / References: UniProt: P31016
#2: Protein/peptide peptide from 5-hydroxytryptamine receptor 2C


Mass: 976.106 Da / Num. of mol.: 1 / Fragment: UNP residues 452-460 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P08909

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HN(CO)CA
1813D HBHA(CO)NH
1913D HBHANH
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11311-D 13C 15N-filtered 1H
11412D 1H-13C HSQC (HB)CB(CGCD)HD
11512D 13C TROSY
11612D 13C-15N F1-filtered NOESY-HSQC
11712D 13C-15N F1-filtered TOCSY
11813D (H)CCH-TOCSY aliphatic
11913D (H)CCH-TOCSY aromatic
12013D 13C,15 F1-filtered 13C F3-edited NOESY-HSQC aliphatic
12113D 13C,15 F1-filtered 13C F3-edited NOESY-HSQC aromatic
12213D 13C,15 F1-filtered 15N F3-edited NOESY-HSQC

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] protein_1, 2.5 mM protein_2, 1 mM DTT, 0.01 w/v sodium azide, 20 mM sodium phosphate, 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity_1-1[U-13C; U-15N]1
2.5 mMentity_2-21
1 mMDTT-31
0.01 w/vsodium azide-41
20 mMsodium phosphate-51
Sample conditionsIonic strength: 20 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CCPN_Analysis2.1CCPNpeak picking
CCPN_Analysis2.1CCPNprocessing
CCPN_Analysis2.1CCPNdata analysis
CCPN_Analysis2.1CCPNchemical shift assignment
DANGLECheung et al, 2010, Journal of Magnetic Resonance, 202, 2: 223-233dihedral angle calculation
CYANArefinement
RefinementMethod: torsion angle dynamics, simulated annealing, simulated annealing
Software ordinal: 1 / Details: in vacuo, water refinement using RECOORD scripts
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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