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- PDB-2dc2: Solution Structure of PDZ Domain -

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Basic information

Entry
Database: PDB / ID: 2dc2
TitleSolution Structure of PDZ Domain
Componentsgolgi associated PDZ and coiled-coil motif containing isoform b
KeywordsSTRUCTURAL PROTEIN / GOPC PDZ domain
Function / homology
Function and homology information


negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / trans-Golgi network transport vesicle / apical protein localization / molecular sequestering activity / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport ...negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / trans-Golgi network transport vesicle / apical protein localization / molecular sequestering activity / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / transmembrane transporter binding / postsynaptic density / lysosomal membrane / Golgi membrane / dendrite / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Golgi-associated PDZ and coiled-coil motif-containing protein / 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
Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsLi, X. / Wu, J. / Shi, Y.
CitationJournal: Protein Sci. / Year: 2006
Title: Solution structure of GOPC PDZ domain and its interaction with the C-terminal motif of neuroligin
Authors: Li, X. / Zhang, J. / Cao, Z. / Wu, J. / Shi, Y.
History
DepositionDec 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: golgi associated PDZ and coiled-coil motif containing isoform b


Theoretical massNumber of molelcules
Total (without water)11,2571
Polymers11,2571
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein golgi associated PDZ and coiled-coil motif containing isoform b / GOPC


Mass: 11256.896 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC gene (270-363) / Plasmid: pET22b (+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HD26

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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: 1.0mM 15N, 13C-labeled GOPC PDZ domain, 10mM phosphate buffer (pH 6.1), 4mM EDTA, 10% (v/v) D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.1 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F.Delaglioprocessing
Sparky3T.D.Goddard and D.G.Knellerdata analysis
CNS1.1A.T.Brungerstructure solution
CSI1David S. Wishartdata analysis
MOLMOL2K.2Koradidata analysis
CNS1.1A.T.Brungerrefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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