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- PDB-7ykg: Crystal structure of MAGI2 PDZ0-GK/pSGEF complex -

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Basic information

Entry
Database: PDB / ID: 7ykg
TitleCrystal structure of MAGI2 PDZ0-GK/pSGEF complex
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
  • SGEF
KeywordsPEPTIDE BINDING PROTEIN / MAGI2 / PDZ0-GK / SGEF / phosphorylated peptide
Function / homology
Function and homology information


type II activin receptor binding / neuroligin clustering involved in postsynaptic membrane assembly / podocyte development / slit diaphragm / positive regulation of synaptic vesicle clustering / beta-1 adrenergic receptor binding / activin receptor binding / nerve growth factor signaling pathway / SMAD protein signal transduction / clathrin-dependent endocytosis ...type II activin receptor binding / neuroligin clustering involved in postsynaptic membrane assembly / podocyte development / slit diaphragm / positive regulation of synaptic vesicle clustering / beta-1 adrenergic receptor binding / activin receptor binding / nerve growth factor signaling pathway / SMAD protein signal transduction / clathrin-dependent endocytosis / negative regulation of activin receptor signaling pathway / ciliary base / SMAD binding / receptor clustering / positive regulation of receptor internalization / photoreceptor outer segment / bicellular tight junction / phosphatase binding / photoreceptor inner segment / centriole / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of cell migration / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / late endosome / signaling receptor complex adaptor activity / postsynaptic density / negative regulation of cell population proliferation / dendrite / synapse / centrosome / perinuclear region of cytoplasm / signal transduction / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Unstructured region on MAGI / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / 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. ...Unstructured region on MAGI / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
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: 2.16 Å
AuthorsZhang, M. / Lin, L. / Zhu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2023
Title: Phosphorylation-dependent recognition of diverse protein targets by the cryptic GK domain of MAGI MAGUKs.
Authors: Zhang, M. / Cao, A. / Lin, L. / Chen, Y. / Shang, Y. / Wang, C. / Zhang, M. / Zhu, J.
History
DepositionJul 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
B: SGEF
C: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
D: SGEF


Theoretical massNumber of molelcules
Total (without water)54,8604
Polymers54,8604
Non-polymers00
Water4,035224
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
B: SGEF


Theoretical massNumber of molelcules
Total (without water)27,4302
Polymers27,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-4 kcal/mol
Surface area10900 Å2
MethodPISA
2
C: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
D: SGEF


Theoretical massNumber of molelcules
Total (without water)27,4302
Polymers27,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-3 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.894, 79.700, 93.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 24 or (resid 25...
22chain C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPRO(chain A and (resid 9 through 24 or (resid 25...AA9 - 245 - 20
22LEULEUchain CCC9 - 1965 - 192

NCS ensembles :
ID
1
2

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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: 25982.301 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 BL21(DE3) (bacteria) / References: UniProt: Q9WVQ1
#2: Protein/peptide SGEF / ARHGEF26


Mass: 1447.558 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride, 0.1 M Tris (pH 8.5), 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97737 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97737 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 27918 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.043 / Rrim(I) all: 0.111 / Χ2: 0.634 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.16-2.196.30.59413630.9840.2520.6470.4699.6
2.19-2.236.40.57413660.9550.2410.6230.46699.9
2.23-2.276.50.48813950.9480.2060.5310.4799.9
2.27-2.326.50.43313410.9620.1820.470.47899.8
2.32-2.376.40.39913860.9760.170.4350.47299.9
2.37-2.426.10.35813750.9740.1570.3920.49499.9
2.42-2.486.10.30913770.9880.1350.3370.49699.9
2.48-2.556.30.27513690.9840.1180.2990.50799.7
2.55-2.626.80.22713870.9950.0940.2460.521100
2.62-2.716.70.20513720.9910.0850.2220.55100
2.71-2.816.70.19813980.9910.0820.2140.578100
2.81-2.926.70.15713900.9930.0650.170.622100
2.92-3.056.50.13313770.9940.0560.1440.69100
3.05-3.216.10.11414040.9930.0510.1250.698100
3.21-3.416.40.09414030.9950.040.1030.8100
3.41-3.686.80.08514020.9960.0350.0920.80499.9
3.68-4.056.70.07414000.9960.0310.080.85999.5
4.05-4.636.20.06314270.9970.0280.0690.90599.8
4.63-5.836.40.06414520.9970.0270.0690.78799.9
5.83-5060.05415340.9980.0230.0590.98199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EEH,5YPO

2eeh

5ypo


Resolution: 2.16→46.52 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 1996 7.17 %
Rwork0.2062 25833 -
obs0.2099 27829 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.89 Å2 / Biso mean: 43.2233 Å2 / Biso min: 19.47 Å2
Refinement stepCycle: final / Resolution: 2.16→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 0 224 3350
Biso mean---44.65 -
Num. residues----400
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1136X-RAY DIFFRACTION5.973TORSIONAL
22C70X-RAY DIFFRACTION5.973TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.210.36341380.27061782192098
2.21-2.270.3271410.268318281969100
2.27-2.340.34691400.241318151955100
2.34-2.410.28431420.233318251967100
2.41-2.50.30741420.231518311973100
2.5-2.60.27791390.217518071946100
2.6-2.720.28821400.219318281968100
2.72-2.860.2781410.222618461987100
2.86-3.040.30221430.215618381981100
3.04-3.270.24641430.208218551998100
3.27-3.60.24411440.195218632007100
3.6-4.120.25181440.178318572001100
4.12-5.190.18511450.17071888203399
5.19-46.520.24371540.21321970212499

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