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- PDB-7ykf: Crystal structure of MAGI2 PDZ0-GK/pEphexin4 complex -

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Basic information

Entry
Database: PDB / ID: 7ykf
TitleCrystal structure of MAGI2 PDZ0-GK/pEphexin4 complex
Components
  • Ephexin4
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
KeywordsPEPTIDE BINDING PROTEIN / MAGI2 / PDZ0-GK / Ephexin4 / phosphorylated peptide
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 / slit diaphragm / positive regulation of synaptic vesicle clustering / 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 / slit diaphragm / positive regulation of synaptic vesicle clustering / 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 / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synaptic membrane adhesion / ciliary base / receptor clustering / SMAD binding / positive regulation of phosphoprotein phosphatase activity / kinesin binding / positive regulation of receptor internalization / photoreceptor outer segment / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / bicellular tight junction / phosphatase binding / photoreceptor inner segment / centriole / negative regulation of cell migration / cellular response to nerve growth factor stimulus / positive regulation of neuron projection development / cell-cell junction / signaling receptor complex adaptor activity / late endosome / postsynaptic density / negative regulation of cell population proliferation / centrosome / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / perinuclear region of cytoplasm / signal transduction / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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. ...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
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: 2.28 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

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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: Ephexin4
C: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
D: Ephexin4


Theoretical massNumber of molelcules
Total (without water)55,0344
Polymers55,0344
Non-polymers00
Water75742
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
B: Ephexin4


Theoretical massNumber of molelcules
Total (without water)27,5172
Polymers27,5172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-5 kcal/mol
Surface area10110 Å2
MethodPISA
2
C: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
D: Ephexin4


Theoretical massNumber of molelcules
Total (without water)27,5172
Polymers27,5172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.209, 55.616, 61.070
Angle α, β, γ (deg.)65.310, 76.620, 71.560
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 15 or (resid 16...
21(chain C and (resid 0 through 4 or (resid 5...
12chain B
22(chain D and resid 231 through 241)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERPROPRO(chain A and (resid 0 through 15 or (resid 16...AA0 - 155 - 20
121GLUGLUGLUGLU(chain A and (resid 0 through 15 or (resid 16...AA1621
131SERSERGLUGLU(chain A and (resid 0 through 15 or (resid 16...AA0 - 1825 - 187
141SERSERGLUGLU(chain A and (resid 0 through 15 or (resid 16...AA0 - 1825 - 187
151SERSERGLUGLU(chain A and (resid 0 through 15 or (resid 16...AA0 - 1825 - 187
161SERSERGLUGLU(chain A and (resid 0 through 15 or (resid 16...AA0 - 1825 - 187
211SERSERSERSER(chain C and (resid 0 through 4 or (resid 5...CC0 - 45 - 9
221LYSLYSLYSLYS(chain C and (resid 0 through 4 or (resid 5...CC510
231SERSERGLUGLU(chain C and (resid 0 through 4 or (resid 5...CC0 - 1825 - 187
241SERSERGLUGLU(chain C and (resid 0 through 4 or (resid 5...CC0 - 1825 - 187
251SERSERGLUGLU(chain C and (resid 0 through 4 or (resid 5...CC0 - 1825 - 187
261SERSERGLUGLU(chain C and (resid 0 through 4 or (resid 5...CC0 - 1825 - 187
112ASNASNMETMETchain BBB231 - 2411 - 11
212ASNASNMETMET(chain D and resid 231 through 241)DD231 - 2411 - 11

NCS ensembles :
ID
1
2

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Components

#1: Protein Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 /


Mass: 25982.301 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) / References: UniProt: Q9WVQ1
#2: Protein/peptide Ephexin4


Mass: 1534.657 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 / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride hexahydrate, 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: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97737 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. obs: 19920 / % possible obs: 97.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Χ2: 0.849 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.28-2.343.10.31710050.9540.2070.380.60695.9
2.34-2.383.20.3289840.9420.2130.3930.53696
2.38-2.433.20.2449780.9640.1590.2920.56496.2
2.43-2.483.10.2479660.9540.1650.2990.61796.6
2.48-2.533.20.23610220.970.1530.2820.65596.7
2.53-2.593.40.2089510.9790.1330.2470.61297
2.59-2.653.50.17810150.9810.1110.2110.66296.7
2.65-2.733.60.1679770.9850.1030.1960.65697
2.73-2.813.50.1489890.9840.0920.1750.68697
2.81-2.93.50.13710110.9860.0860.1620.74498.2
2.9-33.40.1199850.9860.0760.1420.83398
3-3.123.30.09610080.9890.0630.1150.93397.7
3.12-3.263.20.0769970.9930.050.0920.98898.4
3.26-3.433.40.07710090.9930.0490.0911.08698.3
3.43-3.653.50.06810090.9930.0420.081.09798.5
3.65-3.933.50.06210040.9940.0390.0741.18698.6
3.93-4.333.50.0549950.9940.0340.0641.20697.9
4.33-4.953.10.04710050.9960.0310.0571.24898.5
4.95-6.233.50.04910060.9950.0310.0580.97898.2
6.23-303.40.03910040.9960.0250.0460.96598.4

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Processing

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

2eeh

5ypo


Resolution: 2.28→29.67 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 2.43 / Phase error: 31.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1020 5.13 %
Rwork0.1858 18856 -
obs0.1883 19876 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.38 Å2 / Biso mean: 57.0843 Å2 / Biso min: 31.34 Å2
Refinement stepCycle: final / Resolution: 2.28→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 0 42 3021
Biso mean---52.92 -
Num. residues----389
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1104X-RAY DIFFRACTION5.167TORSIONAL
12C1104X-RAY DIFFRACTION5.167TORSIONAL
21B62X-RAY DIFFRACTION5.167TORSIONAL
22D62X-RAY DIFFRACTION5.167TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.28-2.40.31161340.22632575270992
2.4-2.560.31131630.22972658282196
2.56-2.750.23351520.22352670282297
2.75-3.030.27331350.22882741287698
3.03-3.470.27441300.20772738286898
3.47-4.370.23211640.16242732289698
4.37-29.670.18261420.15732742288498
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)
18.6739-0.9946-2.09298.6540.89446.78990.19870.44560.1609-0.7249-0.26880.8106-0.6682-0.06010.03310.4126-0.0083-0.0010.40470.02050.30886.3248-52.3493-34.4588
22.4233-0.9961.6493.1042-0.5415.31410.0682-1.24750.28920.62880.2475-0.65711.22940.5543-0.30090.44970.0875-0.02510.5612-0.06150.698119.8011-66.662-30.5594
35.8430.8173-1.39095.9613-0.89595.71530.4588-0.65730.26721.0196-0.1480.05580.33690.383-0.32340.4853-0.0211-0.03530.4361-0.06150.28729.3924-57.6449-19.447
41.2754-0.6432-1.39713.65171.53286.7369-0.1337-0.2962-0.1379-0.17550.1691-0.3079-0.21950.952-0.23150.439-0.01880.10010.6099-0.05990.40217.9694-56.3099-34.0274
55.31530.0942-2.30048.40161.56085.5896-0.25720.1184-0.2933-0.33790.0830.00860.4197-0.35410.21490.2461-0.0171-0.01760.3016-0.01180.26616.3443-63.9539-29.6002
69.03290.6109-2.33654.97480.57763.2559-0.0302-0.24930.44180.377-0.25340.8491-0.183-0.33670.35020.5817-0.0710.02490.3697-0.08620.4738-0.0514-47.7549-21.6154
74.3310.1125-0.85887.22980.66487.22730.0927-0.48710.44610.5104-0.15670.3966-0.40960.0524-0.02750.3391-0.0648-0.03320.541-0.0770.3544-5.1258-57.3452-23.0994
83.8938-1.24150.69066.45922.89867.31670.7413-0.3480.48430.7563-0.25480.4912-0.8835-0.3283-0.35770.7129-0.08130.21510.3174-0.01390.4078-12.6396-65.1582-4.6514
92.2065-0.7287-2.91133.798-0.48188.18820.5118-0.93351.50841.12650.2181-0.6746-1.65390.7094-0.59781.2196-0.29460.16880.6379-0.06910.6769-3.1874-54.27890.1257
109.569-0.3235-1.68987.28581.92054.45470.7762-0.07820.63740.64-0.38040.951-1.0398-0.155-0.47360.67240.02320.25330.4301-0.02350.5022-7.2952-56.4499-7.9039
114.96014.74462.73494.81921.95476.4868-0.30320.72540.7258-1.57480.27410.73150.6926-0.08120.04380.58470.01960.09870.40460.07060.5897-14.289-59.2082-14.0926
126.5357-0.5307-1.94054.76770.55885.90890.0337-0.6025-0.24880.1520.0003-0.31290.03320.34190.030.4843-0.07520.09450.33510.00280.36181.1777-33.77840.9256
136.68920.3422-2.77295.18850.21425.74660.0662-0.2799-0.52480.2725-0.1990.1096-0.05261.12830.24030.51970.02370.10460.59580.01440.39-1.5823-37.2429.1935
143.9131.8612-0.05575.1563-0.18564.6989-0.16180.24-0.1093-0.2601-0.04020.22280.2521-0.05640.12850.4488-0.05460.10090.30330.00480.3258-0.2974-31.4019-5.5894
158.48012.0337-2.69333.4898-0.99474.24380.53410.65630.6599-0.2752-0.17650.2007-0.03260.4537-0.2150.61940.08930.07220.41810.00590.3544-0.7316-28.4814-14.9248
165.11830.4777-0.8357.4574-0.6636.8107-0.32850.3063-0.5585-0.3190.0348-0.39190.76090.0230.23920.5279-0.0790.16680.3024-0.0710.40815.0359-29.5627-26.7899
177.60131.4490.60327.8971-2.19447.4581-0.49170.1888-0.3063-0.8949-0.1491-0.36220.2717-0.10990.28210.3367-0.02650.1120.3379-0.03950.363712.4038-31.101-23.3331
182.3122-0.3087-0.37597.057-4.4418.9737-0.1943-0.2108-0.02170.1396-0.15451.8282-0.4316-0.4060.36850.526-0.10530.0270.458-0.07760.57544.0946-26.3144-26.6142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 22 )A13 - 22
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 35 )A23 - 35
4X-RAY DIFFRACTION4chain 'A' and (resid 36 through 55 )A36 - 55
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 89 )A56 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 111 )A90 - 111
7X-RAY DIFFRACTION7chain 'A' and (resid 112 through 127 )A112 - 127
8X-RAY DIFFRACTION8chain 'A' and (resid 128 through 150 )A128 - 150
9X-RAY DIFFRACTION9chain 'A' and (resid 151 through 160 )A151 - 160
10X-RAY DIFFRACTION10chain 'A' and (resid 161 through 182 )A161 - 182
11X-RAY DIFFRACTION11chain 'B' and (resid 231 through 241 )B231 - 241
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 35 )C1 - 35
13X-RAY DIFFRACTION13chain 'C' and (resid 36 through 55 )C36 - 55
14X-RAY DIFFRACTION14chain 'C' and (resid 56 through 111 )C56 - 111
15X-RAY DIFFRACTION15chain 'C' and (resid 112 through 127 )C112 - 127
16X-RAY DIFFRACTION16chain 'C' and (resid 128 through 169 )C128 - 169
17X-RAY DIFFRACTION17chain 'C' and (resid 170 through 182 )C170 - 182
18X-RAY DIFFRACTION18chain 'D' and (resid 231 through 242 )D231 - 242

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