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- PDB-5zys: Structure of Nephrin/MAGI1 complex -

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Basic information

Entry
Database: PDB / ID: 5zys
TitleStructure of Nephrin/MAGI1 complex
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
  • Nephrin
KeywordsCELL ADHESION / Slit diaphragm / Nephrotic syndrome / MAGI1- Nephrin complex
Function / homology
Function and homology information


positive regulation of cell-cell adhesion / alpha-actinin binding / bicellular tight junction / cell projection / cell periphery / adherens junction / cell-cell junction / cell junction / nucleolus / signal transduction ...positive regulation of cell-cell adhesion / alpha-actinin binding / bicellular tight junction / cell projection / cell periphery / adherens junction / cell-cell junction / cell junction / nucleolus / signal transduction / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Unstructured region on MAGI / 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 ...Unstructured region on MAGI / 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 / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsWeng, Z.F. / Shng, Y. / Zhu, J.W. / Zhang, R.G.
CitationJournal: J. Am. Soc. Nephrol. / Year: 2018
Title: Structural Basis of Highly Specific Interaction between Nephrin and MAGI1 in Slit Diaphragm Assembly and Signaling.
Authors: Weng, Z. / Shang, Y. / Ji, Z. / Ye, F. / Lin, L. / Zhang, R. / Zhu, J.
History
DepositionMay 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 2.0Dec 11, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: atom_site / diffrn ...atom_site / diffrn / entity / entity_poly / entity_poly_seq / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / refine / refine_hist / refine_ls_shell / reflns / software / struct_sheet_range
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight ..._diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.ls_number_reflns_R_work / _refine.overall_FOM_work_R_set / _refine.pdbx_R_Free_selection_details / _refine.pdbx_method_to_determine_struct / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns.pdbx_number_measured_all / _software.classification / _software.name / _software.version / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Sequence discrepancy
Details: there is one residue mismatch the nephrin sequence. So we replaced the previous sequence (LPFELPGHLV) with the real sequence (LPFELRGHLV) used in the crystal experiment.
Provider: author / Type: Coordinate replacement
Revision 2.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 1
B: Nephrin


Theoretical massNumber of molelcules
Total (without water)11,7582
Polymers11,7582
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-5 kcal/mol
Surface area5710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.731, 93.731, 93.731
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1011-

HOH

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Components

#1: Protein Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 / / BAI1-associated protein 1 / BAP-1 / Membrane-associated guanylate kinase inverted 1 / MAGI-1


Mass: 10576.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Magi1, Baiap1, Bap1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6RHR9
#2: Protein/peptide Nephrin


Mass: 1182.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.5M sodium chloride , 0.01M magnesium chloride hexahydrate , 0.01Mhexadecyltrimethylammonium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 13086 / % possible obs: 98.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 18.68 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.037 / Rrim(I) all: 0.079 / Χ2: 0.754 / Net I/σ(I): 6.2 / Num. measured all: 51381
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.813.60.1726830.9520.1020.2020.56799.9
1.81-1.8440.1676310.9620.0930.1920.58399.2
1.84-1.884.10.1656580.960.0910.1890.67499.1
1.88-1.9240.1436480.9750.0790.1640.72298.5
1.92-1.963.90.1326560.9750.0740.1530.67598.9
1.96-23.90.1276390.9680.0720.1470.71398.9
2-2.053.70.1146700.9750.0650.1320.73999.4
2.05-2.113.80.1026490.9870.0570.1170.77299.8
2.11-2.1740.16510.9810.0550.1150.78999.5
2.17-2.2440.0926630.9820.0510.1060.74499.4
2.24-2.3240.0896770.9820.0490.1020.77799.1
2.32-2.423.90.0856260.9870.0470.0980.79497.4
2.42-2.533.70.0786640.9880.0450.0910.68998.5
2.53-2.6640.0756460.9860.0410.0860.70199.5
2.66-2.8340.0736680.9880.0380.0820.71398.7
2.83-3.0440.0676600.9920.0350.0760.80897.9
3.04-3.353.80.0626340.9910.0340.0710.80996.1
3.35-3.834.10.0576550.9910.030.0650.92697.2
3.83-4.8340.0576400.9930.030.0650.97693.7
4.83-5040.0576680.9940.030.0640.87592.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→46.865 Å / FOM work R set: 0.8774 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 639 4.88 %RANDOM
Rwork0.1812 12444 --
obs0.1822 13083 98.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.85 Å2 / Biso mean: 22.74 Å2 / Biso min: 9.86 Å2
Refinement stepCycle: final / Resolution: 1.78→46.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms773 0 0 88 861
Biso mean---30.97 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006784
X-RAY DIFFRACTIONf_angle_d1.1731063
X-RAY DIFFRACTIONf_chiral_restr0.038118
X-RAY DIFFRACTIONf_plane_restr0.006141
X-RAY DIFFRACTIONf_dihedral_angle_d12.579285
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.78-1.9170.22291290.1858249099
1.917-2.110.1971130.1726250099
2.11-2.41530.20631660.1791245199
2.4153-3.04290.19561240.1872251499
3.0429-46.8650.20691070.1803248995

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