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- PDB-3w9y: Crystal structure of the human DLG1 guanylate kinase domain -

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Basic information

Entry
Database: PDB / ID: 3w9y
TitleCrystal structure of the human DLG1 guanylate kinase domain
ComponentsDisks large homolog 1
KeywordsPEPTIDE BINDING PROTEIN / guanylate kinase / molecular scaffold / peptide binding / cell membrane
Function / homology
Function and homology information


T cell cytokine production / protein-containing complex localization => GO:0031503 / mitotic cell cycle checkpoint signaling / regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization ...T cell cytokine production / protein-containing complex localization => GO:0031503 / mitotic cell cycle checkpoint signaling / regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade / : / guanylate kinase activity / cortical microtubule organization / regulation of sodium ion transmembrane transport / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / NrCAM interactions / lateral loop / reproductive structure development / immunological synapse formation / myelin sheath abaxonal region / receptor localization to synapse / peristalsis / cell projection membrane / Synaptic adhesion-like molecules / smooth muscle tissue development / bicellular tight junction assembly / positive regulation of potassium ion transport / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors / establishment or maintenance of epithelial cell apical/basal polarity / amyloid precursor protein metabolic process / regulation of NMDA receptor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / endothelial cell proliferation / lens development in camera-type eye / mitogen-activated protein kinase kinase binding / Activation of Ca-permeable Kainate Receptor / regulation of myelination / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / establishment or maintenance of cell polarity / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / activation of protein kinase activity / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / receptor clustering / phosphoprotein phosphatase activity / Long-term potentiation / immunological synapse / intercalated disc / negative regulation of mitotic cell cycle / basement membrane / lateral plasma membrane / potassium channel regulator activity / bicellular tight junction / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / T cell proliferation / negative regulation of T cell proliferation / cytoskeletal protein binding / T cell activation / Ras activation upon Ca2+ influx through NMDA receptor / viral process / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / protein localization to plasma membrane / regulation of membrane potential / positive regulation of protein localization to plasma membrane / actin filament organization / adherens junction / postsynaptic density membrane / neuromuscular junction / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / sarcolemma / kinase binding / cell-cell adhesion / negative regulation of epithelial cell proliferation / MAPK cascade / cell-cell junction / cell junction / regulation of cell shape / RAF/MAP kinase cascade / chemical synaptic transmission / basolateral plasma membrane / microtubule / transmembrane transporter binding / molecular adaptor activity / cadherin binding / neuron projection
Similarity search - Function
L27-1 / L27_1 / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / 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 ...L27-1 / L27_1 / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / 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 / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disks large homolog 1 / Disks large homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.2 Å
AuthorsMori, S. / Tezuka, Y. / Arakawa, A. / Handa, N. / Shirouzu, M. / Akiyama, T. / Yokoyama, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structure of the guanylate kinase domain from discs large homolog 1 (DLG1/SAP97)
Authors: Mori, S. / Tezuka, Y. / Arakawa, A. / Handa, N. / Shirouzu, M. / Akiyama, T. / Yokoyama, S.
History
DepositionApr 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large homolog 1


Theoretical massNumber of molelcules
Total (without water)23,4051
Polymers23,4051
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.535, 65.535, 180.563
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Disks large homolog 1 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg


Mass: 23404.502 Da / Num. of mol.: 1 / Fragment: Guanylate kinase domain, UNP residues 734-926
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Plasmid: pCR2.1-TOPO / Production host: Cell-free synthesis (others) / References: UniProt: Q12959-2, UniProt: Q12959*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE ISOFORM 2 FOUND IN UNP Q12959.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium thiocyanate, 22% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979077 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979077 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12192 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Rsym value: 0.077 / Net I/σ(I): 25.3
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.409 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: 1JXO

1jxo


Resolution: 2.2→48 Å / SU ML: 0.36 / σ(F): 2.1 / Phase error: 27.42 / Stereochemistry target values: ML
Details: The structure has also been refined using the program CNS 1.3.
RfactorNum. reflection% reflection
Rfree0.265 1262 10.4 %
Rwork0.209 --
obs0.215 12188 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 0 61 1495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081464
X-RAY DIFFRACTIONf_angle_d1.0011972
X-RAY DIFFRACTIONf_dihedral_angle_d15.722562
X-RAY DIFFRACTIONf_chiral_restr0.067211
X-RAY DIFFRACTIONf_plane_restr0.004257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.280.3862060.321188195
2.28-2.370.3482000.299191096
2.37-2.480.3111700.272197398
2.48-2.610.3382270.256191998
2.61-2.780.3152260.23193398
2.78-2.990.2682180.221195799
2.99-3.290.2432240.196194799
3.29-3.770.2332140.1741976100
3.77-4.740.2182390.1621952100
4.74-48.10.2681960.2091995100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.15292.09-2.92634.76161.75452.53270.24480.46150.5257-0.50170.28580.1326-0.27670.5691-0.55410.3721-0.1135-0.01870.3974-0.09320.3533-19.90830.47722.3413
21.65112.03311.41712.41411.07711.61660.18550.2520.17320.0232-0.01690.03060.0130.7378-0.04480.285-0.0747-0.01150.5306-0.07560.3172-19.304319.4787-4.1745
34.9757-0.5901-1.99993.8761-0.76096.77680.0626-0.0891-0.1751-0.04920.2653-0.00481.50340.2189-0.33910.46240.0698-0.10650.3931-0.05820.3362-28.12639.356-6.4187
41.8857-0.89620.42921.8749-1.24478.37730.0381-0.222-0.1754-0.03390.2610.20831.1117-0.6197-0.17250.2444-0.076-0.01770.40350.03530.2989-34.855815.0812-0.5298
58.74763.58890.53375.70091.20524.5087-0.3011-0.514-0.3921-0.13950.2684-0.86340.43640.62320.09250.20890.04250.00110.411-0.04610.2915-20.220519.09855.4154
64.81962.4544-0.2654.2552-0.11152.08610.0232-0.34570.80.16950.20970.6216-0.0866-0.095-0.18220.30120.03390.03580.5586-0.04880.3851-27.111927.63210.7337
73.67583.75171.89273.91382.28882.09260.13590.70582.2727-1.50670.09672.4438-0.6674-1.21480.06950.65780.15360.01410.67950.32491.5135-32.70644.273-0.6371
84.43480.23093.08491.3118-2.0676.02-0.1655-1.24650.7310.52010.03811.6228-1.0276-2.43720.01550.45310.08750.06460.922-0.36871.0509-32.302935.986610.508
95.6708-0.4104-5.52563.4150.47289.07311.56070.0282.3487-0.2783-0.19960.3486-2.290.6864-1.15680.8078-0.17240.18470.6485-0.05831.0059-18.810844.09932.3245
102.4508-2.95850.71826.0881-2.35864.8738-0.5355-0.07981.5506-0.1689-0.096-0.7408-0.87130.92120.3860.3426-0.1575-0.01930.5863-0.08450.5753-13.658537.41876.0898
113.82983.9819-3.35425.5801-1.49997.21050.42330.0779-0.6021-0.1129-0.5883-0.38540.0927-1.19170.15310.28820.04880.00640.3875-0.08860.2873-3.11232.380510.0075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 734:753)
2X-RAY DIFFRACTION2chain A and (resseq 754:773)
3X-RAY DIFFRACTION3chain A and (resseq 774:793)
4X-RAY DIFFRACTION4chain A and (resseq 794:813)
5X-RAY DIFFRACTION5chain A and (resseq 814:833)
6X-RAY DIFFRACTION6chain A and (resseq 834:853)
7X-RAY DIFFRACTION7chain A and (resseq 854:881)
8X-RAY DIFFRACTION8chain A and (resseq 882:891)
9X-RAY DIFFRACTION9chain A and (resseq 892:901)
10X-RAY DIFFRACTION10chain A and (resseq 902:911)
11X-RAY DIFFRACTION11chain A and (resseq 912:926)

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