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- PDB-1q56: NMR structure of the B0 isoform of the agrin G3 domain in its Ca2... -

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Basic information

Entry
Database: PDB / ID: 1q56
TitleNMR structure of the B0 isoform of the agrin G3 domain in its Ca2+ bound state
ComponentsAgrin
KeywordsMETAL BINDING PROTEIN / NMJ synapse / mRNA splicing / AChR aggregation / laminin-G like domain / conformational flexibility / MuSK activation / Ca2+ regulation
Function / homology
Function and homology information


extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / photoreceptor ribbon synapse / dystroglycan binding ...extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / photoreceptor ribbon synapse / dystroglycan binding / basal part of cell / filopodium assembly / glycosaminoglycan binding / extracellular matrix binding / heparan sulfate proteoglycan binding / positive regulation of filopodium assembly / neuromuscular junction development / transmembrane receptor protein tyrosine kinase activator activity / receptor clustering / basement membrane / laminin binding / extracellular matrix / brain development / neuromuscular junction / G protein-coupled acetylcholine receptor signaling pathway / positive regulation of GTPase activity / negative regulation of neuron projection development / signaling receptor activity / heparin binding / nervous system development / actin cytoskeleton organization / cell differentiation / membrane raft / axon / synapse / glutamatergic synapse / calcium ion binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin G domain / Laminin-type EGF-like (LE) domain profile. ...NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Kazal-type serine protease inhibitor domain / SEA domain superfamily / Laminin-type EGF domain / SEA domain profile. / Kazal-type serine protease inhibitor domain / SEA domain / SEA domain / Laminin G domain profile. / Kazal type serine protease inhibitors / Laminin G domain / Laminin G domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / Torsion angle dynamics (Dyana 1.5), simulated annealing (X-Plor 3.851)
AuthorsStetefeld, J. / Alexandrescu, A.T. / Maciejewski, M.W. / Jenny, M. / Rathgeb-Szabo, K. / Schulthess, T. / Landwehr, R. / Frank, S. / Ruegg, M.A. / Kammerer, R.A.
CitationJournal: Structure / Year: 2004
Title: Modulation of agrin function by alternative splicing and Ca2+ binding
Authors: Stetefeld, J. / Alexandrescu, A.T. / Maciejewski, M.W. / Jenny, M. / Rathgeb-Szabo, K. / Schulthess, T. / Landwehr, R. / Frank, S. / Ruegg, M.A. / Kammerer, R.A.
History
DepositionAug 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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: Agrin


Theoretical massNumber of molelcules
Total (without water)21,3331
Polymers21,3331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Agrin /


Mass: 21333.219 Da / Num. of mol.: 1 / Fragment: 195 a.a. C-terminal domain, G3 domain
Mutation: extra GS at N-terminus (residues 1,2) from cloning artifact
Source method: isolated from a genetically manipulated source
Details: B0 isoform / Source: (gene. exp.) Gallus gallus (chicken) / Gene: AGRN / Plasmid: pGSTHis, a derivative of pGEX-1 (Amersham) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P31696

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY (100 ms)
121HNHB (chi restraints)
131HSQC-NOESY-HSQC (tm = 200 ms / perdeuterated protein)
141HN(CA)CB (TALOS restraints from HN,Ca, Cb shifts ), HNCO (Talos C' shifts), 3D-15N sep TOCSY (Talos Ha shifts)
1523D-13C separated NOESY (tm = 125 ms) and isotope exchange experiments to derive H-bond restraints
NMR detailsText: sample for 15N HSQC-NOESY 15N HSQC was 2H/13C/15N labeled.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM protein, 5 mM CaCl2, 10 mM d4-immidazole90% H2O/10% D2O
21 mM protein, 5 mM CaCl2, 10 mM d4-immidazole99.9% D2O
Sample conditionsIonic strength: 5 mM CaCl2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Gntertstructure solution
X-PLOR3.851Brungerrefinement
Felix2000?accelerysdata analysis
RefinementMethod: Torsion angle dynamics (Dyana 1.5), simulated annealing (X-Plor 3.851)
Software ordinal: 1
Details: Hydrogen bond restraints were assigned based on protection from solvent exchange, and consistency of hydrogen bonds with preliminary structures. Backbone phi and psi dihedral restraints were ...Details: Hydrogen bond restraints were assigned based on protection from solvent exchange, and consistency of hydrogen bonds with preliminary structures. Backbone phi and psi dihedral restraints were obtained from 1Ha, 13Ca, 13Cb, 13C and 15N chemical shifts using the program TALOS (Cornilescu et al., 1993). Side-chain chi1 restraints were from 3D HNHB data, in conjunction with HN-HBETA 2/HN-HBETA 3 and HALPHA-HBETA 2/HALPHA-HBETA 3 NOE intensity ratios. These data were also used to obtain stereospecific assignments for the C-BETA protons of 37 residues. NOEs involving the remainder of prochiral groups with non-degenerate chemical shifts were treated as ambiguous with respect to stereospecific assignments, and represented as 1/^-1/6 sums using XPLOR 3.851 (Brunger, 1992). Initial structures calculated with this approach, were used to identify sites in which one of the stereospecific assignments was more consistent with the remaining distance and dihedral restraints. This enabled stereospecific assignment of a further 13 methylene groups, and 13 valine and leucine prochiral methyl groups. For the final NMR calculations, 400 random conformations were subjected to restrained torsion angle dynamics with the program Dyana 1.5 (Guentert et al., 1997). The 40 structures with the smallest Dyana target functions were refined with a published simulated annealing protocol (Nilges et al., 1991), using the program XPLOR 3.851 (Brunger, 1992). The 15 lowest-energy simulated annealing structures with no distance or dihedral violations larger than 4 were kept for analysis.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 15

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