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- PDB-3uat: Guanylate Kinase Domains of the MAGUK Family Scaffold Proteins as... -

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Basic information

Entry
Database: PDB / ID: 3uat
TitleGuanylate Kinase Domains of the MAGUK Family Scaffold Proteins as Specific Phospho-Protein Binding Modules
Components
  • Disks large homolog 1
  • phosphor-LGN peptide
KeywordsPEPTIDE BINDING PROTEIN / DLG GK domain / phosphor-peptide binding module / phosphor-LGN
Function / homology
Function and homology information


tissue morphogenesis / 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 / lateral cell cortex / maintenance of centrosome location / membrane raft organization / hard palate development ...tissue morphogenesis / 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 / lateral cell cortex / maintenance of centrosome location / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade / structural constituent of postsynaptic density / astral microtubule organization / embryonic skeletal system morphogenesis / positive regulation of spindle assembly / reproductive structure development / epithelial structure maintenance / immunological synapse formation / lateral loop / myelin sheath abaxonal region / receptor localization to synapse / lung epithelial cell differentiation / peristalsis / cell projection membrane / cortical microtubule organization / smooth muscle tissue development / paranode region of axon / bicellular tight junction assembly / Trafficking of AMPA receptors / positive regulation of potassium ion transport / Activation of Ca-permeable Kainate Receptor / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / amyloid precursor protein metabolic process / Synaptic adhesion-like molecules / GDP-dissociation inhibitor activity / RAF/MAP kinase cascade / G alpha (i) signalling events / endothelial cell proliferation / lens development in camera-type eye / ureteric bud development / regulation of myelination / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / dynein complex binding / receptor clustering / mitotic spindle pole / establishment of mitotic spindle orientation / kinesin binding / microvillus / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / G-protein alpha-subunit binding / bicellular tight junction / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic density, intracellular component / phosphatase binding / potassium channel regulator activity / positive regulation of protein localization to cell cortex / negative regulation of T cell proliferation / T cell proliferation / regulation of mitotic spindle organization / cellular response to brain-derived neurotrophic factor stimulus / T-tubule / ionotropic glutamate receptor binding / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitotic spindle organization / basal plasma membrane / regulation of membrane potential / T cell activation / actin filament organization / protein localization to plasma membrane / synaptic membrane / PDZ domain binding / positive regulation of protein localization to plasma membrane / postsynaptic density membrane / neuromuscular junction / cerebral cortex development / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / synaptic vesicle membrane / cytoplasmic side of plasma membrane / negative regulation of epithelial cell proliferation / cell-cell junction / protein localization / cell junction / apical part of cell / regulation of protein localization / presynaptic membrane / regulation of cell shape
Similarity search - Function
: / GoLoco motif / L27-1 / GoLoco motif / L27_1 / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Tetratricopeptide repeat ...: / GoLoco motif / L27-1 / GoLoco motif / L27_1 / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Tetratricopeptide repeat / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Tetratricopeptide repeat / 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 / Tetratricopeptide repeat / 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. / Tetratricopeptide repeat / SH3 Domains / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
G-protein signaling modulator 2 / Disks large homolog 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShang, Y. / Zhu, J. / Wen, W. / Zhang, M.
CitationJournal: Embo J. / Year: 2011
Title: Guanylate kinase domains of the MAGUK family scaffold proteins as specific phospho-protein-binding modules
Authors: Zhu, J. / Shang, Y. / Xia, C. / Wang, W. / Wen, W. / Zhang, M.
History
DepositionOct 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disks large homolog 1
B: phosphor-LGN peptide


Theoretical massNumber of molelcules
Total (without water)36,5512
Polymers36,5512
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-10 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.566, 66.155, 55.155
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34296.691 Da / Num. of mol.: 1 / Fragment: UNP residues 578-911
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg1, Dlgh1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62696
#2: Protein/peptide phosphor-LGN peptide


Mass: 2254.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: D3ZCE5*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6.8
Details: 0.2M Sodium nitrate, 20% w/v Polyethylene glycol 3350 , pH 6.8, EVAPORATION, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9817 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9817 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 9300 / Num. obs: 9281 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 42.42 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.449 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.811 / SU ML: 0.58 / σ(F): 1.34 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2415 442 4.77 %
Rwork0.1868 --
obs0.1896 9268 99.69 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.723 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 136.49 Å2 / Biso mean: 55.0607 Å2 / Biso min: 10.29 Å2
Baniso -1Baniso -2Baniso -3
1-6.2732 Å2-0 Å24.4113 Å2
2---3.7112 Å20 Å2
3----2.562 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 36 2325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032341
X-RAY DIFFRACTIONf_angle_d0.7653178
X-RAY DIFFRACTIONf_dihedral_angle_d13.798862
X-RAY DIFFRACTIONf_chiral_restr0.056351
X-RAY DIFFRACTIONf_plane_restr0.002419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6999-3.09050.32051430.23912921
3.0905-3.89350.27081510.19362922
3.8935-46.45540.1981480.1652983
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)
13.0293-1.45630.39084.1202-1.14963.36-0.09060.0128-1.12010.00750.24410.06550.65340.5634-0.14610.25990.1170.03840.535-0.09740.797613.1709-32.18913.9183
24.3522-4.9755-2.76519.06870.7153.58140.0674-0.2123-1.2962-0.33980.2248-0.61820.68571.4405-0.14770.38090.19290.06260.67-0.13550.910916.0555-34.719517.4102
39.6202-3.4483-5.78799.01971.10117.2737-0.8556-0.6259-2.19620.0949-0.0202-0.53731.16170.98630.81150.45720.1142-0.00760.47110.03010.680311.4986-35.298122.8301
45.29450.085-3.90061.6291-2.24248.54010.16120.3712-0.0772-0.350.0125-0.14050.05591.2115-0.16180.3631-0.02240.06120.5937-0.04470.528517.0808-25.682313.169
52.3112-0.63870.22825.2438-0.26923.76990.13530.1003-0.0970.4119-0.1980.5044-0.1099-0.46080.35520.33720.01310.14090.2612-0.00850.3023-8.8189-17.02915.9962
61.3405-0.3683-0.5185.7661-0.93571.97680.08720.0091-0.01720.2663-0.25530.267-0.283-0.15150.18290.3763-0.00050.05360.2954-0.02890.1948-7.5845-0.881616.0561
71.9498-0.21510.72492.76081.97417.91980.34430.43560.0339-0.2598-0.2162-0.0577-0.4742-0.061-0.00840.35390.08480.16160.25390.02740.36-3.0125-20.29762.3032
82.60380.00492.72741.83061.83889.29850.0287-0.06330.08760.4257-0.16110.08460.5594-0.1368-0.14890.3873-0.0160.11240.1371-0.01940.331-2.6908-24.956517.6444
97.1338-0.855-2.92064.71331.28417.9841-0.30671.2943-0.8002-0.6321-0.56170.63360.2522-0.75120.62280.57550.04820.02170.3365-0.22780.3402-6.9793-1.81577.3098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 582:597)A582 - 597
2X-RAY DIFFRACTION2chain 'A' and (resseq 598:621)A598 - 621
3X-RAY DIFFRACTION3chain 'A' and (resseq 622:637)A622 - 637
4X-RAY DIFFRACTION4chain 'A' and (resseq 638:717)A638 - 717
5X-RAY DIFFRACTION5chain 'A' and (resseq 718:741)A718 - 741
6X-RAY DIFFRACTION6chain 'A' and (resseq 742:827)A742 - 827
7X-RAY DIFFRACTION7chain 'A' and (resseq 828:874)A828 - 874
8X-RAY DIFFRACTION8chain 'A' and (resseq 875:908)A875 - 908
9X-RAY DIFFRACTION9chain 'B'B-2 - 12

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