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- PDB-5b64: A novel binding mode of MAGUK GK domain revealed by DLG GK domain... -

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Basic information

Entry
Database: PDB / ID: 5b64
TitleA novel binding mode of MAGUK GK domain revealed by DLG GK domain in complex with KIF13B MBS domain
Components
  • DLG GK
  • Protein Kif13b
KeywordsPEPTIDE BINDING PROTEIN / MAGUK / GK / KIF13B / MBS / Kinesin / Motor
Function / homology
Function and homology information


RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / embryo development / receptor localization to synapse / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / paranode region of axon / LGI-ADAM interactions / Trafficking of AMPA receptors / dendritic branch / neuron spine / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / dendritic spine morphogenesis / juxtaparanode region of axon / frizzled binding / negative regulation of receptor internalization / dendritic spine organization / neuron projection terminus / acetylcholine receptor binding / postsynaptic neurotransmitter receptor diffusion trapping / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / regulation of NMDA receptor activity / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / microtubule motor activity / kinesin complex / regulation of axonogenesis / cortical cytoskeleton / microtubule-based movement / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / positive regulation of excitatory postsynaptic potential / microvillus / social behavior / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / positive regulation of protein tyrosine kinase activity / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / beta-2 adrenergic receptor binding / extrinsic component of cytoplasmic side of plasma membrane / 14-3-3 protein binding / dendrite cytoplasm / synaptic membrane / PDZ domain binding / cell periphery / postsynaptic density membrane / ionotropic glutamate receptor binding / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cerebral cortex development / kinase binding / cell-cell adhesion / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / postsynapse / microtubule binding / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / microtubule / dendritic spine / postsynaptic density / neuron projection / axon / signaling receptor binding / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding
Similarity search - Function
: / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. ...: / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / 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 / Kinesin-associated / PDZ-associated domain of NMDA receptors / Kinesin-associated / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / FHA domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / Kinesin motor domain superfamily / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinesin family member 13B / Disks large homolog 4
Similarity search - Component
Biological speciesRattus (rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShang, Y. / Zhu, J. / Zhang, M.
CitationJournal: Structure / Year: 2016
Title: An Atypical MAGUK GK Target Recognition Mode Revealed by the Interaction between DLG and KIF13B
Authors: Zhu, J. / Shang, Y. / Xia, Y. / Zhang, R. / Zhang, M.
History
DepositionMay 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DLG GK
B: Protein Kif13b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,17710
Polymers36,4162
Non-polymers7618
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-70 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.279, 116.279, 72.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-801-

SO4

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Components

#1: Protein DLG GK


Mass: 21690.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus (rat) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31016*PLUS
#2: Protein Protein Kif13b


Mass: 14725.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif13b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E9Q4K7
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.0M Ammonium sulfate, 0.1M HEPES pH 7.0, 0.5%(w/v) Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.7→36.8 Å / Num. obs: 13026 / % possible obs: 97.8 % / Redundancy: 3.8 % / Net I/σ(I): 25.8

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→36.771 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.48
RfactorNum. reflection% reflection
Rfree0.2458 643 4.94 %
Rwork0.1871 --
obs0.19 13024 97.8 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 61.836 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.464 Å20 Å2-0 Å2
2--0.464 Å20 Å2
3----0.9281 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 42 29 2348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082353
X-RAY DIFFRACTIONf_angle_d1.0693189
X-RAY DIFFRACTIONf_dihedral_angle_d16.097848
X-RAY DIFFRACTIONf_chiral_restr0.07355
X-RAY DIFFRACTIONf_plane_restr0.005412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.90870.33041330.29132495X-RAY DIFFRACTION99
2.9087-3.20120.28941330.22822473X-RAY DIFFRACTION99
3.2012-3.66410.26371280.18742517X-RAY DIFFRACTION99
3.6641-4.61490.21361310.15892476X-RAY DIFFRACTION98
4.6149-36.7740.23921180.18412420X-RAY DIFFRACTION93
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)
12.6525-3.3994-2.68536.64990.0418.748-0.0365-0.37130.25110.4807-0.08830.0571-1.1288-0.15340.06070.738-0.06650.0860.6464-0.00190.50821.2371-36.0618-45.5556
23.5445-0.6102-2.12917.6165-1.08528.20810.16740.40910.0260.1421-0.10290.23430.0038-0.5371-0.09390.42670.00230.05770.56690.02490.5939-10.9619-41.5637-30.7829
33.3309-0.35090.90495.9416-1.43649.4911-0.26580.1481-0.39790.13030.18310.3830.8711-0.48260.0070.49640.01140.17090.5019-0.06640.6933-7.7846-46.8744-35.4319
44.4527-2.5333-4.53618.91111.15884.6494-0.04051.2942-0.6629-0.7669-0.34710.91020.7244-0.82780.46980.6393-0.04030.05880.8242-0.11780.6769-4.1707-45.5787-46.1922
53.5691.88413.95398.18072.14788.27040.3922-0.15040.37070.67550.4101-1.6269-1.09222.0809-0.44140.645-0.40240.02080.9655-0.21020.737515.8968-36.8485-46.4844
64.18580.91126.42748.33260.55412.17810.01180.6676-1.21930.1333-0.1993-1.1904-0.26082.12140.06980.6746-0.02360.04961.45280.02780.954114.9358-46.6515-44.1769
73.26840.5497-0.79497.85521.43815.36390.73791.26010.8269-0.7883-0.5218-0.7144-1.80171.0787-0.21820.975-0.14750.19960.91140.19460.6836.7388-34.892-53.8547
82.9812-0.2773-0.33536.0440.47095.21820.1640.25360.3209-0.434-0.192-0.1166-0.73370.1142-0.07410.4409-0.0227-0.00790.46390.11380.5814-5.4357-13.0523-20.5742
97.9442-4.2643-3.95242.64160.74569.44781.64630.06710.70721.14950.3329-0.04672.1479-1.3272-1.84860.9006-0.2264-0.04660.98710.54061.2662-25.677-9.491-14.8608
108.0802-6.1135-6.53446.30185.09976.74430.58030.5609-0.0514-0.1382-0.66080.3892-0.1328-0.96510.26980.8157-0.05970.0190.71120.03230.7552-17.0167-9.3432-20.7797
113.82-1.9786-0.32337.54092.08664.39990.0985-0.6168-0.55970.63610.13020.47250.1115-0.216-0.32210.5442-0.00880.04580.43080.12820.5788-5.4279-24.6242-20.5597
128.2114.98261.37462.10386.83765.07120.1716-0.1432-1.16730.14990.4343-1.32060.27780.7088-0.54430.5060.040.0260.4427-0.02990.80141.8064-38.4005-30.2505
136.09444.0057-0.38554.92462.68753.80920.41891.69770.8745-0.1822-1.04182.03390.0667-0.89130.45540.69350.0793-0.0080.754-0.03750.8066-11.378-25.8252-29.269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 533:554)
2X-RAY DIFFRACTION2chain 'A' and (resseq 555:594)
3X-RAY DIFFRACTION3chain 'A' and (resseq 595:621)
4X-RAY DIFFRACTION4chain 'A' and (resseq 622:645)
5X-RAY DIFFRACTION5chain 'A' and (resseq 646:666)
6X-RAY DIFFRACTION6chain 'A' and (resseq 667:687)
7X-RAY DIFFRACTION7chain 'A' and (resseq 688:712)
8X-RAY DIFFRACTION8chain 'B' and (resseq 680:718)
9X-RAY DIFFRACTION9chain 'B' and (resseq 719:725)
10X-RAY DIFFRACTION10chain 'B' and (resseq 726:746)
11X-RAY DIFFRACTION11chain 'B' and (resseq 747:772)
12X-RAY DIFFRACTION12chain 'B' and (resseq 773:786)
13X-RAY DIFFRACTION13chain 'B' and (resseq 787:795)

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