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- PDB-7d6f: The crystal structure of ARMS-PBM/MAGI2-PDZ4 -

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Basic information

Entry
Database: PDB / ID: 7d6f
TitleThe crystal structure of ARMS-PBM/MAGI2-PDZ4
Components
  • Kinase D-interacting substrate of 220 kDa
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
KeywordsSTRUCTURAL PROTEIN / PBM/PDZ interaction / scaffold protein / synaptic polaricity
Function / homology
Function and homology information


ARMS-mediated activation / 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 ...ARMS-mediated activation / 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 / protein kinase regulator activity / clathrin-dependent endocytosis / negative regulation of activin receptor signaling pathway / SMAD protein signal transduction / dendrite morphogenesis / 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 / cellular response to nerve growth factor stimulus / negative regulation of cell migration / PDZ domain binding / positive regulation of neuron projection development / cell-cell junction / signaling receptor complex adaptor activity / late endosome / in utero embryonic development / postsynaptic density / membrane => GO:0016020 / negative regulation of cell population proliferation / centrosome / dendrite / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / signal transduction / protein-containing complex / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
KAP family P-loop domain / KAP family P-loop domain / Unstructured region on MAGI / Domain of unknown function DUF3447 / 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 ...KAP family P-loop domain / KAP family P-loop domain / Unstructured region on MAGI / Domain of unknown function DUF3447 / 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 / Sterile alpha motif/pointed domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinase D-interacting substrate of 220 kDa / Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsYe, J. / Zhang, Y. / Zhong, Z. / Wang, C.
CitationJournal: Neurochem.Int. / Year: 2021
Title: Crystal structure of the PDZ4 domain of MAGI2 in complex with PBM of ARMS reveals a canonical PDZ recognition mode.
Authors: Zhang, Y. / Zhong, Z. / Ye, J. / Wang, C.
History
DepositionSep 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 1, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / citation_author / database_2 / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _audit_author.name / _chem_comp.formula ..._audit_author.name / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_starting_model / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.pdbx_number_measured_all / _software.version / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_sheet.number_strands
Description: Real space R-factor
Details: To cut off the high resolution to 3.0 Angstrom when running the refinement program.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 17, 2021Group: 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 / _citation_author.name
Revision 2.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Kinase D-interacting substrate of 220 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8123
Polymers12,7202
Non-polymers921
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-7 kcal/mol
Surface area5240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.045, 95.666, 35.167
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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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: 10793.422 Da / Num. of mol.: 1
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 Kinase D-interacting substrate of 220 kDa / ARMS / Ankyrin repeat-rich membrane-spanning protein


Mass: 1926.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kidins220, Arms / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EQG6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 3696 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 83.67 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.027 / Rrim(I) all: 0.096 / Χ2: 0.684 / Net I/σ(I): 4.9 / Num. measured all: 46340
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.7511.80.7241780.9670.2190.7570.485100
2.75-2.812.60.9741640.8680.2841.0150.491100
2.8-2.8512.20.6321820.9710.1850.6590.506100
2.85-2.9112.30.6941920.9520.2040.7240.51100
2.91-2.9713.30.6341700.9610.1790.660.484100
2.97-3.0413.40.5181880.9790.1440.5380.511100
3.04-3.1213.60.4251710.9730.1170.4410.53100
3.12-3.213.50.3132030.9930.0880.3250.528100
3.2-3.313.40.2511620.9930.070.2610.562100
3.3-3.412.90.1691860.9980.050.1770.614100
3.4-3.5213.40.1661850.9950.0470.1730.649100
3.52-3.6612.60.151770.9950.0440.1560.708100
3.66-3.8312.20.1091880.9980.0320.1140.765100
3.83-4.0311.30.1031850.9960.0310.1080.807100
4.03-4.2911.90.081800.9980.0240.0840.944100
4.29-4.6212.90.0731900.9980.0210.0761.095100
4.62-5.0812.90.0591970.9970.0170.0620.873100
5.08-5.8112.80.0611860.9980.0180.0640.797100
5.81-7.3211.50.0621940.9980.0190.0650.773100
7.32-5010.50.0472180.9990.0140.0491.05499.5

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Processing

Software
NameVersionClassification
PHENIXv1.13refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
MOLREP3.25phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZYS

5zys


Resolution: 3.001→29.277 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 20.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2814 137 5.09 %
Rwork0.2353 2552 -
obs0.2381 2689 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.29 Å2 / Biso mean: 90.6272 Å2 / Biso min: 33.88 Å2
Refinement stepCycle: final / Resolution: 3.001→29.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms657 0 6 3 666
Biso mean--134.18 63.16 -
Num. residues----96
LS refinement shellResolution: 3→3.61 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2814 137 -
Rwork0.2353 2552 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -10.3215 Å / Origin y: -15.8526 Å / Origin z: 6.0889 Å
111213212223313233
T0.5429 Å20.0955 Å2-0.0938 Å2-0.5709 Å2-0.2705 Å2--0.6016 Å2
L13.9231 °211.3462 °2-3.7456 °2-6.8912 °2-4.0202 °2--1.1742 °2
S-0.6112 Å °-1.9994 Å °2.1955 Å °-0.0172 Å °0.1679 Å °0.8567 Å °0.1862 Å °0.7536 Å °0.0882 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA916 - 1008
2X-RAY DIFFRACTION1allB1754 - 1762
3X-RAY DIFFRACTION1allC1 - 3
4X-RAY DIFFRACTION1allD1

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