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

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Basic information

Entry
Database: PDB / ID: 7yki
TitleCrystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR3 peptide
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
  • SAPAP1
KeywordsPEPTIDE BINDING PROTEIN / MAGI2 / PDZ0-GK / SAPAP1 / GBR3 / 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
PHOSPHATE ION / 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 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 1.2Oct 9, 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

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Assembly

Deposited unit
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
C: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
B: SAPAP1
D: SAPAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,08112
Polymers55,3384
Non-polymers7438
Water4,468248
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
B: SAPAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1357
Polymers27,6692
Non-polymers4665
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-12 kcal/mol
Surface area10500 Å2
MethodPISA
2
C: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
D: SAPAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9455
Polymers27,6692
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-9 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.975, 78.909, 92.997
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
32B
42D

NCS domain segments:

End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERAA9 - 1915 - 187
211SERSERCB9 - 1915 - 187
322ILEILEBC-4 - 71 - 12
422ILEILEDD-4 - 71 - 12

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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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: 1686.782 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 2.1 M ammonium phosphate dibasic, 0.2 M ammonium sulfate, 0.1M Tris (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32529 / % possible obs: 97.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.091 / Χ2: 2.279 / Net I/σ(I): 12.9 / Num. measured all: 138910
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.034.40.50616231.59198.9
2.03-2.074.30.45216192.015198.2
2.07-2.114.40.39516231.691199.3
2.11-2.154.40.34416221.731198.9
2.15-2.24.40.316241.879198.9
2.2-2.254.30.28816102.13197.8
2.25-2.314.40.22316481.927199.1
2.31-2.374.40.19916411.956199.2
2.37-2.444.40.18416292.042198.6
2.44-2.524.40.16216292.1198.1
2.52-2.614.40.14516172.172198.3
2.61-2.714.40.12716392.296197.5
2.71-2.844.40.10916342.329198.3
2.84-2.994.30.08716392.642198.3
2.99-3.174.20.07416152.694197
3.17-3.424.10.06316393.066197.1
3.42-3.763.90.05416033.299195
3.76-4.313.80.04516033.188194.5
4.31-5.433.90.04116202.81193.5
5.43-5040.03616522.521189.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EEH,5YPO

2eeh

5ypo


Resolution: 2→44.496 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.198 / SU B: 4.173 / SU ML: 0.114 / Average fsc free: 0.9559 / Average fsc work: 0.9699 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.168
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2486 1601 4.93 %
Rwork0.2074 30873 -
all0.209 --
obs-32474 96.94 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.078 Å2
Baniso -1Baniso -2Baniso -3
1-4.342 Å20 Å2-0 Å2
2---2.295 Å2-0 Å2
3----2.047 Å2
Refinement stepCycle: LAST / Resolution: 2→44.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 46 248 3300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123128
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162846
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6564242
X-RAY DIFFRACTIONr_angle_other_deg0.4961.5646639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.674518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46610503
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.14310133
X-RAY DIFFRACTIONr_chiral_restr0.0670.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
X-RAY DIFFRACTIONr_nbd_refined0.2170.2638
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22610
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21537
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2480.2231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1520.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1310.222
X-RAY DIFFRACTIONr_nbd_other0.1780.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.213
X-RAY DIFFRACTIONr_mcbond_it2.8872.9041564
X-RAY DIFFRACTIONr_mcbond_other2.8832.9041564
X-RAY DIFFRACTIONr_mcangle_it4.3294.3311950
X-RAY DIFFRACTIONr_mcangle_other4.3294.3341951
X-RAY DIFFRACTIONr_scbond_it3.9283.3671564
X-RAY DIFFRACTIONr_scbond_other3.9273.371565
X-RAY DIFFRACTIONr_scangle_it6.0974.8432288
X-RAY DIFFRACTIONr_scangle_other6.0964.8462289
X-RAY DIFFRACTIONr_lrange_it8.68245.0713542
X-RAY DIFFRACTIONr_lrange_other8.57844.5163484
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.055705
X-RAY DIFFRACTIONr_ncsr_local_group_20.1470.05299
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.058870.05009
12AX-RAY DIFFRACTIONLocal ncs0.058870.05009
23AX-RAY DIFFRACTIONLocal ncs0.146590.05006
24AX-RAY DIFFRACTIONLocal ncs0.146590.05006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3411080.27922130.28124290.9290.94495.55370.22
2.052-2.1080.2881150.25722310.25823770.9140.9598.69580.202
2.108-2.1690.2671040.24121880.24223110.9460.96199.17780.196
2.169-2.2360.2761110.22720970.22922470.9530.96698.26440.18
2.236-2.3090.292940.21520280.21821590.9520.9798.28620.173
2.309-2.390.2281060.20519860.20621220.9620.97498.58620.171
2.39-2.480.231070.19919050.220500.9660.97798.14630.158
2.48-2.5810.2341010.19518240.19719520.9690.97898.61680.159
2.581-2.6950.251820.20217620.20418800.9680.97698.08510.17
2.695-2.8260.242820.18617010.18818240.9620.9897.75220.16
2.826-2.9780.256790.18416140.18717210.9590.97998.3730.165
2.978-3.1580.2910.19115030.19216450.9770.97896.89970.181
3.158-3.3750.226800.20514230.20615410.9610.97597.53410.2
3.375-3.6440.209720.19413060.19514380.9670.97795.82750.188
3.644-3.9890.175640.18511960.18413430.9840.9893.81980.191
3.989-4.4550.213610.17710840.17912190.970.98293.92950.2
4.455-5.1360.339380.1899820.19310960.9370.9893.06570.21
5.136-6.2690.283570.248220.2439230.9660.96995.23290.27
6.269-8.7790.347320.2336580.2377500.9420.965920.269
8.779-44.4960.335170.2833500.2864600.9320.94279.78260.327

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