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- PDB-3wp1: Phosphorylation-dependent interaction between tumor suppressors D... -

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Basic information

Entry
Database: PDB / ID: 3wp1
TitlePhosphorylation-dependent interaction between tumor suppressors Dlg and Lgl
Components
  • Disks large homolog 4
  • Lethal(2) giant larvae protein homolog 2
KeywordsPEPTIDE BINDING PROTEIN / MaGuk / Phosphorylation / Cell polarity / tumor suppressors / phosphorylation dependent
Function / homology
Function and homology information


establishment of spindle orientation / regulation of establishment or maintenance of cell polarity / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density ...establishment of spindle orientation / regulation of establishment or maintenance of cell polarity / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / L-leucine transport / positive regulation of neuron projection arborization / regulation of grooming behavior / regulation of Notch signaling pathway / receptor localization to synapse / myosin II binding / vocalization behavior / cerebellar mossy fiber / LGI-ADAM interactions / proximal dendrite / Golgi to plasma membrane transport / neuron spine / Trafficking of AMPA receptors / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / AMPA glutamate receptor clustering / cellular response to potassium ion / Activation of Ca-permeable Kainate Receptor / dendritic branch / positive regulation of dendrite morphogenesis / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / frizzled binding / acetylcholine receptor binding / neuron projection terminus / dendritic spine organization / regulation of NMDA receptor activity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / NMDA selective glutamate receptor signaling pathway / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / cortical actin cytoskeleton organization / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical actin cytoskeleton / cortical cytoskeleton / exocytosis / social behavior / locomotory exploration behavior / AMPA glutamate receptor complex / regulation of neuronal synaptic plasticity / neuromuscular process controlling balance / kinesin binding / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / GTPase activator activity / cell periphery / PDZ domain binding / adherens junction / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / neuromuscular junction / cerebral cortex development / cell-cell adhesion / kinase binding / cell junction / synaptic vesicle / cell-cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / signaling receptor binding / cell division / intracellular membrane-bounded organelle / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / membrane
Similarity search - Function
Lethal(2) giant larvae protein / Lethal giant larvae homologue 2 / LLGL2 / 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 / : ...Lethal(2) giant larvae protein / Lethal giant larvae homologue 2 / LLGL2 / 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 / Trp-Asp (WD) repeats signature. / P-loop containing nucleotide triphosphate hydrolases / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disks large homolog 4 / LLGL scribble cell polarity complex component 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsZhu, J. / Shang, Y. / Wan, Q. / Xia, Y. / Chen, J. / Du, Q. / Zhang, M.
CitationJournal: Cell Res. / Year: 2014
Title: Phosphorylation-dependent interaction between tumor suppressors Dlg and Lgl
Authors: Zhu, J. / Shang, Y. / Wan, Q. / Xia, Y. / Chen, J. / Du, Q. / Zhang, M.
History
DepositionJan 8, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Oct 16, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Disks large homolog 4
A: Lethal(2) giant larvae protein homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0916
Polymers23,7072
Non-polymers3844
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-7 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.518, 161.518, 45.032
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-802-

SO4

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Components

#1: Protein Disks large homolog 4 / Postsynaptic density protein 95 / PSD-95 / Synapse-associated protein 90 / SAP-90 / SAP90


Mass: 21414.131 Da / Num. of mol.: 1 / Fragment: UNP residues 531-713
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Production host: Escherichia coli (E. coli) / References: UniProt: P31016
#2: Protein/peptide Lethal(2) giant larvae protein homolog 2 / HGL


Mass: 2292.695 Da / Num. of mol.: 1 / Fragment: UNP residues 646-657 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6P1M3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.58 Å3/Da / Density % sol: 65.61 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97893 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 8937 / Num. obs: 8915 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.804→42.865 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 425 4.77 %
Rwork0.1992 --
obs0.2024 8908 99.71 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.275 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.7261 Å20 Å20 Å2
2---8.7261 Å2-0 Å2
3---17.4521 Å2
Refinement stepCycle: LAST / Resolution: 2.804→42.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 20 4 1565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091586
X-RAY DIFFRACTIONf_angle_d1.152140
X-RAY DIFFRACTIONf_dihedral_angle_d17.352593
X-RAY DIFFRACTIONf_chiral_restr0.084230
X-RAY DIFFRACTIONf_plane_restr0.004278
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
2.804-3.20930.31681380.26692735
3.2093-4.04290.28731460.19352787
4.0429-42.87040.24361410.18692961
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)
16.2961-2.06850.39673.1651.72481.63150.37670.6796-0.33150.0836-0.19640.11590.36110.19440.17030.93830.4428-0.47630.02450.170.5316135.9828155.17988.3347
24.776-2.22-2.55433.50851.70231.4635-0.34010.1785-0.0889-0.7756-0.0980.4111-0.39-0.45450.4620.71380.0933-0.15190.43120.04550.5147147.5851149.5224-2.8181
33.3098-2.9568-0.86063.70321.11446.2278-0.12470.36511.2181-1.03070.588-0.4303-1.17060.489-0.19190.991-0.112-0.00440.40720.30140.5754157.4399155.7952-2.9515
44.48091.61311.1584.20631.45014.8908-0.04420.15781.7808-0.62230.1474-0.9753-0.8021-0.6447-0.25310.77150.1126-0.04140.40330.14010.7832151.4595158.91021.2727
54.0824-0.1338-3.08388.22574.29335.02971.16830.21130.59460.35840.6892-1.15740.59290.5612-1.1750.75980.1738-0.14680.52770.00310.9901143.2317162.7896.8148
66.0478-1.4687-1.29064.62940.5193.2048-0.0348-0.9433-0.00291.15240.21540.17260.3729-0.3953-0.38911.16610.0199-0.09470.57660.18090.4728135.7407155.921519.4618
77.0541-2.62670.92114.2695-1.30244.08820.1741-0.99950.26811.06950.19790.22010.4035-0.4722-0.16770.94110.1177-0.19380.3816-0.03330.4561134.7519158.218919.2344
88.7263-3.7454-3.63712.11762.05152.3523-0.52420.5769-0.53-1.8817-0.07470.6258-1.0151-0.71370.15450.874-0.1331-0.03340.84470.02550.3535145.2119144.5911-2.1531
92.9567-1.1234-2.97352.69811.33123.0617-0.6351-0.676-0.18661.52930.37960.54460.13970.3022-0.12270.5890.116-0.07810.55870.04420.4872150.9458147.6357.5698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 533:554)
2X-RAY DIFFRACTION2chain 'B' and (resseq 555:574)
3X-RAY DIFFRACTION3chain 'B' and (resseq 575:594)
4X-RAY DIFFRACTION4chain 'B' and (resseq 595:622)
5X-RAY DIFFRACTION5chain 'B' and (resseq 623:640)
6X-RAY DIFFRACTION6chain 'B' and (resseq 641:666)
7X-RAY DIFFRACTION7chain 'B' and (resseq 667:712)
8X-RAY DIFFRACTION8chain 'A' and (resseq -5:-1)
9X-RAY DIFFRACTION9chain 'A' and (resseq 0:6)

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