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- PDB-3wp0: Crystal structure of Dlg GK in complex with a phosphor-Lgl2 peptide -

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Basic information

Entry
Database: PDB / ID: 3wp0
TitleCrystal structure of Dlg GK in complex with a phosphor-Lgl2 peptide
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: 2.039 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 1.2Nov 13, 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
A: Disks large homolog 4
B: Lethal(2) giant larvae protein homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9219
Polymers23,2762
Non-polymers6457
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-12 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.082, 84.082, 65.883
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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 533-713
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: 1862.139 Da / Num. of mol.: 1 / Fragment: UNP residues 640-654 / Source method: obtained synthetically / Details: LLGL2 / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6P1M3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2M lithium chloride, 20% PEG3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 30, 2012
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17523 / % possible obs: 99 % / 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: 2.039→42.041 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 888 5.08 %RANDOM
Rwork0.1657 ---
obs0.1674 17494 99.79 %-
all-17523 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.714 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3115 Å20 Å2-0 Å2
2--5.3115 Å20 Å2
3----10.623 Å2
Refinement stepCycle: LAST / Resolution: 2.039→42.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 42 149 1755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111639
X-RAY DIFFRACTIONf_angle_d1.212200
X-RAY DIFFRACTIONf_dihedral_angle_d13.285622
X-RAY DIFFRACTIONf_chiral_restr0.099237
X-RAY DIFFRACTIONf_plane_restr0.006284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0391-2.16690.25351510.1992271499
2.1669-2.33420.23831460.19322737100
2.3342-2.56910.24641590.18032724100
2.5691-2.94070.21771550.1812737100
2.9407-3.70470.20011410.15422812100
3.7047-42.04990.17071360.15582882100
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)
10.2217-0.0989-0.00255.4747-0.58762.5526-0.01230.00090.0021-0.01870.04360.32310.2221-0.1926-0.03090.1647-0.10260.01620.29330.01180.192325.8827-34.4330.4739
21.1019-1.5013-0.64166.1372-0.65561.88390.04420.11560.1429-0.1932-0.0304-0.276-0.03080.0827-0.02570.2103-0.10690.01990.31760.00730.259631.6648-27.6439-1.2201
37.5407-0.36991.15383.87220.0899.1086-0.3292-0.75230.01110.51540.1820.0567-0.84950.23630.13020.4777-0.01820.00610.19650.01470.27528.5793-14.699411.5392
42.41262.55911.45954.8381-1.86666.368-0.0116-0.02530.160.36860.03620.12760.06970.5057-0.08160.3345-0.02750.02510.2998-0.00960.257631.1405-35.913310.7847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 533:594)
2X-RAY DIFFRACTION2chain 'A' and (resseq 595:654)
3X-RAY DIFFRACTION3chain 'A' and (resseq 655:713)
4X-RAY DIFFRACTION4chain 'B' and (resseq 571:584)

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