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- PDB-7ykh: Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho... -

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Basic information

Entry
Database: PDB / ID: 7ykh
TitleCrystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR2 peptide
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
  • SAPAP1
KeywordsPEPTIDE BINDING PROTEIN / MAGI2 / PDZ0-GK / SAPAP1 / GBR2 / 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 / nerve growth factor signaling pathway / activin receptor binding / 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 / nerve growth factor signaling pathway / activin receptor binding / 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 / synapse / dendrite / 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: 2.5 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 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: 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 13, 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: SAPAP1
C: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
D: SAPAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4625
Polymers55,3704
Non-polymers921
Water64936
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
B: SAPAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7773
Polymers27,6852
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-4 kcal/mol
Surface area10050 Å2
MethodPISA
2
C: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
D: SAPAP1


Theoretical massNumber of molelcules
Total (without water)27,6852
Polymers27,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-5 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.212, 61.540, 65.104
Angle α, β, γ (deg.)90.000, 101.790, 90.000
Int Tables number4
Space group name H-MP1211

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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 SAPAP1


Mass: 1702.823 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 25% w/v PEG 3350, 0.1 M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14863 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.107 / Χ2: 2.186 / Net I/σ(I): 8.8 / Num. measured all: 108108
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.5-2.547.30.6297231.442199.9
2.54-2.597.40.627471.471100
2.59-2.647.30.467401.552199.6
2.64-2.697.40.4947211.5631100
2.69-2.757.40.4457571.525199.6
2.75-2.827.40.3897371.619199.6
2.82-2.897.30.3287321.787199.9
2.89-2.967.30.2887521.702199.9
2.96-3.057.30.2417441.874199.9
3.05-3.157.30.1967232.071199.4
3.15-3.267.30.1527452.161199.9
3.26-3.397.30.1337302.192199.9
3.39-3.557.20.1097312.266199.9
3.55-3.7370.0997612.519199.3
3.73-3.9770.0877332.708198.9
3.97-4.277.40.0747512.9041100
4.27-4.77.30.0657563.0131100
4.7-5.387.40.0647432.8481100
5.38-6.787.30.0697582.966199.9
6.78-506.90.0567793.56198.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EEH,5YPO

2eeh

5ypo


Resolution: 2.5→40.609 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 751 5.08 %
Rwork0.2038 27246 -
obs0.2071 14805 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.61 Å2 / Biso mean: 48.16 Å2 / Biso min: 26.72 Å2
Refinement stepCycle: final / Resolution: 2.5→40.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 6 36 3048
Biso mean--63.35 43.51 -
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083083
X-RAY DIFFRACTIONf_angle_d1.1614184
X-RAY DIFFRACTIONf_chiral_restr0.068463
X-RAY DIFFRACTIONf_plane_restr0.007545
X-RAY DIFFRACTIONf_dihedral_angle_d15.9111147
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkRefine-IDRfactor Rfree error% reflection obs (%)
2.5-2.59120.34470.2659X-RAY DIFFRACTION098
2.5912-2.69490.36090.2617X-RAY DIFFRACTION099
2.6949-2.81760.3590.2553X-RAY DIFFRACTION099
2.8176-2.96610.31570.262X-RAY DIFFRACTION099
2.9661-3.15180.30550.2382X-RAY DIFFRACTION099
3.1518-3.39510.27190.2128X-RAY DIFFRACTION0100
3.3951-3.73650.30040.2044X-RAY DIFFRACTION0100
3.7365-4.27670.25490.1752X-RAY DIFFRACTION099
4.2767-5.38620.18970.1661X-RAY DIFFRACTION0100
5.3862-40.6090.24790.1854X-RAY DIFFRACTION099

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