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- PDB-1pdr: CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN FROM THE HUMAN HOMOLOG ... -

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Entry
Database: PDB / ID: 1pdr
TitleCRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN FROM THE HUMAN HOMOLOG OF DISCS LARGE PROTEIN
ComponentsHUMAN DISCS LARGE PROTEIN
KeywordsSIGNAL TRANSDUCTION / SH3 DOMAIN
Function / homology
Function and homology information


L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / myelin sheath abaxonal region / structural constituent of postsynaptic density / GMP kinase activity ...L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / myelin sheath abaxonal region / structural constituent of postsynaptic density / GMP kinase activity / NrCAM interactions / embryonic skeletal system morphogenesis / astral microtubule organization / reproductive structure development / immunological synapse formation / membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of p38MAPK cascade / peristalsis / receptor localization to synapse / lateral loop / smooth muscle tissue development / cell projection membrane / bicellular tight junction assembly / cortical microtubule organization / regulation of sodium ion transmembrane transport / Synaptic adhesion-like molecules / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of potassium ion transport / regulation of ventricular cardiac muscle cell action potential / Trafficking of AMPA receptors / hard palate development / protein-containing complex localization / node of Ranvier / amyloid precursor protein metabolic process / endothelial cell proliferation / Assembly and cell surface presentation of NMDA receptors / lens development in camera-type eye / cortical actin cytoskeleton organization / regulation of myelination / Activation of Ca-permeable Kainate Receptor / branching involved in ureteric bud morphogenesis / neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of G1/S transition of mitotic cell cycle / receptor clustering / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / phosphoprotein phosphatase activity / basement membrane / Long-term potentiation / intercalated disc / immunological synapse / lateral plasma membrane / bicellular tight junction / potassium channel regulator activity / phosphatase binding / T cell proliferation / regulation of postsynaptic membrane neurotransmitter receptor levels / cytoskeletal protein binding / negative regulation of T cell proliferation / actin filament polymerization / ionotropic glutamate receptor binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / actin filament organization / protein localization to plasma membrane / regulation of membrane potential / positive regulation of protein localization to plasma membrane / adherens junction / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell-cell adhesion / postsynaptic density membrane / sarcolemma / negative regulation of ERK1 and ERK2 cascade / kinase binding / cytoplasmic side of plasma membrane / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / nervous system development / regulation of cell shape / RAF/MAP kinase cascade / basolateral plasma membrane / chemical synaptic transmission / molecular adaptor activity / microtubule / transmembrane transporter binding / neuron projection / apical plasma membrane / cadherin binding / membrane raft / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse
Similarity search - Function
L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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 ...L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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 / : / 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 / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Disks large homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsCabral, J.M. / Liddington, R.
Citation
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Clustering Membrane Proteins: It'S All Coming Together with the Psd-95/Sap90 Protein Family
Authors: Gomperts, S.N.
#2: Journal: Trends Biochem.Sci. / Year: 1995
Title: Dhr Domains in Syntrophins, Neuronal No Synthases and Other Intracellular Proteins
Authors: Ponting, C.P. / Phillips, C.
#3: Journal: Nature / Year: 1995
Title: Clustering of Shaker-Type K+ Channels by Interaction with a Family of Membrane-Associated Guanylate Kinases
Authors: Kim, E. / Niethammer, M. / Rothschild, A. / Jan, Y.N. / Sheng, M.
History
DepositionJul 26, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 26, 2016Group: Other
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN DISCS LARGE PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,5571
Polymers10,5571
Non-polymers00
Water1448
1
A: HUMAN DISCS LARGE PROTEIN
x 6


Theoretical massNumber of molelcules
Total (without water)63,3406
Polymers63,3406
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Unit cell
Length a, b, c (Å)110.970, 110.970, 62.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein HUMAN DISCS LARGE PROTEIN / HDLG / DHR3 DOMAIN


Mass: 10556.708 Da / Num. of mol.: 1 / Fragment: PDZ3 DOMAIN, DHR3 DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE THIRD PDZ DOMAIN OF THE HUMAN HOMOLOGUE OF DISCS LARGE PROTEIN
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q12959
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.26 Å3/Da / Density % sol: 76.61 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.9-1.3 Msodium citrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 12, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 5911 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.108
Reflection
*PLUS
Highest resolution: 2.8 Å
Reflection shell
*PLUS
Rmerge(I) obs: 0.301

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.8→10 Å / σ(F): 2
Details: SER 517 IS POSITIONED IN A VERY TIGHT LOOP AND THERE IS CLEAR DENSITY FOR ITS MAIN CHAIN ATOMS. THE PHI AND PSI ANGLES FOR THIS RESIDUE ARE OUTSIDE THE EXPECTED RANGE. THE DEPOSITORS ...Details: SER 517 IS POSITIONED IN A VERY TIGHT LOOP AND THERE IS CLEAR DENSITY FOR ITS MAIN CHAIN ATOMS. THE PHI AND PSI ANGLES FOR THIS RESIDUE ARE OUTSIDE THE EXPECTED RANGE. THE DEPOSITORS ATTEMPTED REPEATEDLY TO REGULARIZE THEM BUT THEY ALWAYS REFINED TO THE SAME VALUES.
RfactorNum. reflection
Rfree0.271 -
Rwork0.22 -
obs0.22 5793
Displacement parametersBiso mean: 16.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms719 0 0 8 727
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4

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