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

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Basic information

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 / establishment of centrosome localization / NrCAM interactions / GMP kinase activity / structural constituent of postsynaptic density / membrane repolarization during ventricular cardiac muscle cell action potential ...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 / establishment of centrosome localization / NrCAM interactions / GMP kinase activity / structural constituent of postsynaptic density / membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of p38MAPK cascade / receptor localization to synapse / myelin sheath abaxonal region / lateral loop / cell projection membrane / bicellular tight junction assembly / endothelial cell proliferation / establishment or maintenance of epithelial cell apical/basal polarity / cortical microtubule organization / astral microtubule organization / regulation of sodium ion transmembrane transport / Synaptic adhesion-like molecules / protein localization to synapse / protein-containing complex localization / Trafficking of AMPA receptors / positive regulation of potassium ion transport / regulation of ventricular cardiac muscle cell action potential / cortical actin cytoskeleton organization / node of Ranvier / Assembly and cell surface presentation of NMDA receptors / negative regulation of G1/S transition of mitotic cell cycle / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / establishment or maintenance of cell polarity / basement membrane / immunological synapse / Long-term potentiation / intercalated disc / lateral plasma membrane / bicellular tight junction / potassium channel regulator activity / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphatase binding / cytoskeletal protein binding / phosphoprotein phosphatase activity / ionotropic glutamate receptor binding / protein localization to plasma membrane / Ras activation upon Ca2+ influx through NMDA receptor / actin filament organization / positive regulation of protein localization to plasma membrane / synaptic membrane / adherens junction / neuromuscular junction / cell-cell adhesion / negative regulation of ERK1 and ERK2 cascade / regulation of membrane potential / sarcolemma / cell junction / postsynaptic density membrane / kinase binding / cytoplasmic side of plasma membrane / regulation of cell shape / cell-cell junction / nervous system development / RAF/MAP kinase cascade / chemical synaptic transmission / molecular adaptor activity / basolateral plasma membrane / microtubule / transmembrane transporter binding / apical plasma membrane / neuron projection / cadherin binding / membrane raft / protein kinase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / glutamatergic synapse / Golgi apparatus / endoplasmic reticulum / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
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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