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- PDB-6jjz: Crystal Structure of MAGI2 and Dendrin complex -

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Basic information

Entry
Database: PDB / ID: 6jjz
TitleCrystal Structure of MAGI2 and Dendrin complex
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
  • Peptide from Dendrin
KeywordsSIGNALING PROTEIN / WW tandem / PY tandem / MAGI2 / Dendrin
Function / homology
Function and homology information


structural constituent of postsynaptic specialization / extrinsic component of postsynaptic membrane / type II activin receptor binding / neuroligin clustering involved in postsynaptic membrane assembly / podocyte development / positive regulation of synaptic vesicle clustering / slit diaphragm / beta-1 adrenergic receptor binding / structural constituent of postsynaptic density / nerve growth factor signaling pathway ...structural constituent of postsynaptic specialization / extrinsic component of postsynaptic membrane / type II activin receptor binding / neuroligin clustering involved in postsynaptic membrane assembly / podocyte development / positive regulation of synaptic vesicle clustering / slit diaphragm / beta-1 adrenergic receptor binding / structural constituent of postsynaptic density / nerve growth factor signaling pathway / activin receptor binding / clathrin-dependent endocytosis / negative regulation of activin receptor signaling pathway / SMAD protein signal transduction / dendritic spine membrane / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synaptic membrane adhesion / ciliary base / SMAD binding / receptor clustering / kinesin binding / positive regulation of phosphoprotein phosphatase activity / positive regulation of receptor internalization / photoreceptor outer segment / GABA-ergic synapse / bicellular tight junction / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatase binding / centriole / photoreceptor inner segment / negative regulation of cell migration / cellular response to nerve growth factor stimulus / cell projection / positive regulation of neuron projection development / cell-cell junction / signaling receptor complex adaptor activity / late endosome / postsynaptic membrane / perikaryon / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / centrosome / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Dendrin / Nephrin and CD2AP-binding protein, Dendrin / Unstructured region on MAGI / 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. ...Dendrin / Nephrin and CD2AP-binding protein, Dendrin / Unstructured region on MAGI / 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. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / Dendrin / Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLin, Z. / Zhang, H. / Yang, Z. / Ji, Z. / Zhang, M. / Zhu, J.
CitationJournal: Elife / Year: 2019
Title: Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.
Authors: Lin, Z. / Yang, Z. / Xie, R. / Ji, Z. / Guan, K. / Zhang, M.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
C: Peptide from Dendrin
D: Peptide from Dendrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0817
Polymers27,8664
Non-polymers2143
Water2,594144
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
C: Peptide from Dendrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9923
Polymers13,9332
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-10 kcal/mol
Surface area7160 Å2
MethodPISA
2
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
D: Peptide from Dendrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0884
Polymers13,9332
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-23 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.899, 58.582, 86.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 / / Activin receptor-interacting protein 1 / Acvrip1 / Atrophin-1-interacting protein 1 / AIP-1 / ...Activin receptor-interacting protein 1 / Acvrip1 / Atrophin-1-interacting protein 1 / AIP-1 / Membrane-associated guanylate kinase inverted 2 / MAGI-2


Mass: 12089.212 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Magi2, Acvrinp1, Aip1, Arip1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WVQ1
#2: Protein/peptide Peptide from Dendrin /


Mass: 1843.966 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ddn, Gm748, Kiaa0749 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80TS7
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: 2.0-2.5M ammonium sulfate, 100mM sodium acetate (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 29381 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 44
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1465 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YSD

2ysd


Resolution: 1.65→27.917 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 27.42
RfactorNum. reflection% reflection
Rfree0.2379 1443 4.92 %
Rwork0.2041 --
obs0.2058 29302 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→27.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 13 144 1850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061762
X-RAY DIFFRACTIONf_angle_d1.0032413
X-RAY DIFFRACTIONf_dihedral_angle_d12.218648
X-RAY DIFFRACTIONf_chiral_restr0.037242
X-RAY DIFFRACTIONf_plane_restr0.005322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6481-1.7070.31921350.27242709X-RAY DIFFRACTION98
1.707-1.77540.25691410.23082745X-RAY DIFFRACTION100
1.7754-1.85620.25991350.2242744X-RAY DIFFRACTION100
1.8562-1.9540.281700.21862737X-RAY DIFFRACTION100
1.954-2.07640.26981570.2132744X-RAY DIFFRACTION100
2.0764-2.23660.26881230.20962814X-RAY DIFFRACTION100
2.2366-2.46160.24761430.21282783X-RAY DIFFRACTION100
2.4616-2.81750.25241430.22332791X-RAY DIFFRACTION100
2.8175-3.54860.24211420.21392850X-RAY DIFFRACTION100
3.5486-27.92060.20331540.17662942X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -9.2337 Å / Origin y: -5.2763 Å / Origin z: 13.4028 Å
111213212223313233
T0.2345 Å20.0398 Å20.0223 Å2-0.16 Å2-0.0017 Å2--0.2193 Å2
L1.0526 °20.2242 °21.2495 °2-0.2719 °20.4112 °2--3.088 °2
S-0.0206 Å °-0.0377 Å °-0.0067 Å °-0.0512 Å °0.0375 Å °-0.0376 Å °0.0405 Å °0.1017 Å °-0.035 Å °
Refinement TLS groupSelection details: all

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