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- PDB-2kpk: MAGI-1 PDZ1 -

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Basic information

Entry
Database: PDB / ID: 2kpk
TitleMAGI-1 PDZ1
ComponentsMembrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
KeywordsPROTEIN BINDING / PDZ domain / ATP-binding / Cell junction / Cell membrane / Membrane / Nucleotide-binding / Phosphoprotein / Tight junction
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 / protein-containing complex assembly / cell surface receptor signaling pathway ...positive regulation of cell-cell adhesion / alpha-actinin binding / bicellular tight junction / cell projection / cell periphery / adherens junction / cell-cell junction / cell junction / protein-containing complex assembly / cell surface receptor signaling pathway / cell adhesion / nucleolus / signal transduction / nucleoplasm / ATP binding / 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. / PDZ domain / Pdz3 Domain / 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 / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsCharbonnier, S. / Nomine, Y. / Ramirez, J. / Luck, K. / Stote, R.H. / Trave, G. / Kieffer, B. / Atkinson, R.A.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: The structural and dynamic response of MAGI-1 PDZ1 with non-canonical domain boundaries to binding of human papillomavirus (HPV) E6
Authors: Charbonnier, S. / Nomine, Y. / Ramirez, J. / Luck, K. / Chapelle, A. / Stote, R.H. / Trave, G. / Kieffer, B. / Atkinson, R.A.
#1: Journal: J.Biomol.Nmr / Year: 2006
Title: 13C, 15N and 1H resonance assignment of the PDZ1 domain of MAGI-1 using QUASI
Authors: Charbonnier, S. / Coutouly, M.A. / Kieffer, B. / Trave, G. / Atkinson, R.A.
History
DepositionOct 16, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)13,8721
Polymers13,8721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 64structures with the lowest energy
RepresentativeModel #1lowest energy

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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 / ...BAI1-associated protein 1 / BAP-1 / Membrane-associated guanylate kinase inverted 1 / MAGI-1 / Atrophin-1-interacting protein 3 / AIP3 / WW domain-containing protein 3 / WWP3 / Trinucleotide repeat-containing gene 19 protein


Mass: 13871.819 Da / Num. of mol.: 1 / Fragment: UNP residues 455-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAGI1, BAIAP1, BAP1, TNRC19 / Plasmid: pETM-41 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QZ7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D HN(CO)CA
1233D HNCA
1333D HN(COCA)CB
1433D HN(CA)CB
1533D HNCO
1633D (H)CCH-TOCSY
1733D (H)CCH-COSY
1823D 1H-15N NOESY
1923D 1H-15N TOCSY
11023D 1H-13C NOESY
11112D 1H-1H TOCSY
11212D 1H-1H NOESY
11322D 15N T1
11422D 15N T2
11522D 1H-15N NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-0.6mM MAGI-1 PDZ1-1, 0.02-0.10mM sodium phosphate-2, 50mM sodium chloride-3, 2mM DTT-4, 90% H2O/10% D2O90% H2O/10% D2O
20.2-0.6mM [U-15N] MAGI-1 PDZ1-5, 0.02-0.10mM sodium phosphate-6, 50mM sodium chloride-7, 2mM DTT-8, 90% H2O/10% D2O90% H2O/10% D2O
30.2-0.6mM [U-100% 13C; U-100% 15N] MAGI-1 PDZ1-9, 0.02-0.10mM sodium phosphate-10, 50mM sodium chloride-11, 2mM DTT-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMMAGI-1 PDZ1-10.2-0.61
mMsodium phosphate-20.02-0.101
50 mMsodium chloride-31
2 mMDTT-41
mMMAGI-1 PDZ1-5[U-15N]0.2-0.62
mMsodium phosphate-60.02-0.102
50 mMsodium chloride-72
2 mMDTT-82
mMMAGI-1 PDZ1-9[U-100% 13C; U-100% 15N]0.2-0.63
mMsodium phosphate-100.02-0.103
50 mMsodium chloride-113
2 mMDTT-123
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
XEASYCARABartels et al.chemical shift assignment
ATNOS-CANDIDHerrmann, Guntert, Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: NMR_WATERREFINE protocol
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 64 / Conformers submitted total number: 20 / Representative conformer: 1

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