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- PDB-4wiq: The structure of Murine alpha-Dystroglycan T190M mutant N-termina... -

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Basic information

Entry
Database: PDB / ID: 4wiq
TitleThe structure of Murine alpha-Dystroglycan T190M mutant N-terminal domain.
ComponentsDystroglycan
KeywordsSTRUCTURAL PROTEIN / mutant / dystroglycanopathy
Function / homology
Function and homology information


O-linked glycosylation / dystroglycan complex / nerve maturation / muscle attachment / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / Regulation of expression of SLITs and ROBOs / contractile ring / regulation of gastrulation / microtubule anchoring ...O-linked glycosylation / dystroglycan complex / nerve maturation / muscle attachment / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / Regulation of expression of SLITs and ROBOs / contractile ring / regulation of gastrulation / microtubule anchoring / calcium-dependent cell-matrix adhesion / morphogenesis of an epithelial sheet / dystrophin-associated glycoprotein complex / laminin-1 binding / response to denervation involved in regulation of muscle adaptation / basement membrane organization / positive regulation of myelination / regulation of epithelial to mesenchymal transition / skeletal muscle tissue regeneration / dystroglycan binding / cellular response to cholesterol / nerve development / vinculin binding / photoreceptor ribbon synapse / myelination in peripheral nervous system / branching involved in salivary gland morphogenesis / node of Ranvier / costamere / angiogenesis involved in wound healing / commissural neuron axon guidance / response to muscle activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic cytosol / axon regeneration / positive regulation of cell-matrix adhesion / structural constituent of muscle / negative regulation of MAPK cascade / epithelial tube branching involved in lung morphogenesis / positive regulation of oligodendrocyte differentiation / regulation of synapse organization / alpha-actinin binding / plasma membrane raft / membrane protein ectodomain proteolysis / cellular response to organic cyclic compound / basement membrane / GABA-ergic synapse / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Schwann cell development / heart morphogenesis / laminin binding / tubulin binding / SH2 domain binding / negative regulation of cell migration / nuclear periphery / filopodium / morphogenesis of an epithelium / adherens junction / axon guidance / regulation of synaptic plasticity / sarcolemma / response to peptide hormone / cellular response to mechanical stimulus / cell-cell junction / protein transport / lamellipodium / virus receptor activity / heart development / actin binding / postsynapse / basolateral plasma membrane / postsynaptic membrane / cytoskeleton / membrane raft / external side of plasma membrane / focal adhesion / glutamatergic synapse / calcium ion binding / protein-containing complex binding / cell surface / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Dystroglycan, domain 2 / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. ...Dystroglycan, domain 2 / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. / Putative Ig domain / Cadherin-like superfamily / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBrancaccio, A. / Lamba, D. / Cassetta, A. / Bozzi, M. / Covaceuszach, S. / Sciandra, F. / Bigotti, M.G.
CitationJournal: Plos One / Year: 2015
Title: The Structure of the T190M Mutant of Murine alpha-Dystroglycan at High Resolution: Insight into the Molecular Basis of a Primary Dystroglycanopathy.
Authors: Bozzi, M. / Cassetta, A. / Covaceuszach, S. / Bigotti, M.G. / Bannister, S. / Hubner, W. / Sciandra, F. / Lamba, D. / Brancaccio, A.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6695
Polymers28,4471
Non-polymers2224
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-1 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.879, 71.879, 144.296
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

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Components

#1: Protein Dystroglycan / Dystrophin-associated glycoprotein 1


Mass: 28447.400 Da / Num. of mol.: 1 / Fragment: UNP residues 50-313 / Mutation: R166H, T190M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dag1, Dag-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q62165
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.24 % / Description: regular slabs
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution: 5.25 mg/mL in 25 mM Tris, 150 mM NaCl and 2.5 % glycerol; pH 7.5 Precipitant solution: 0.8 M citrate buffer; pH 7.0 Drops volume: 1 microL protein solution + 1 microL ...Details: Protein solution: 5.25 mg/mL in 25 mM Tris, 150 mM NaCl and 2.5 % glycerol; pH 7.5 Precipitant solution: 0.8 M citrate buffer; pH 7.0 Drops volume: 1 microL protein solution + 1 microL precipitant solution Reservoir volume: 1 mL Crystals appeared after few days

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→48.1 Å / Num. all: 35504 / Num. obs: 35504 / % possible obs: 95 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 20.41 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 15.28
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.74 / % possible all: 71.8

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Processing

Software
NameVersionClassification
XDSjanuary 10, 2014data reduction
Aimless0.2.17data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UC2

1uc2


Resolution: 1.59→48.099 Å / SU ML: 0.14 / SU R Cruickshank DPI: 0.0863 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1632 1784 5.02 %
Rwork0.1461 --
obs0.147 35504 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.71 Å2
Refinement stepCycle: LAST / Resolution: 1.59→48.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 13 194 1948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011846
X-RAY DIFFRACTIONf_angle_d1.2452523
X-RAY DIFFRACTIONf_dihedral_angle_d11.655690
X-RAY DIFFRACTIONf_chiral_restr0.053292
X-RAY DIFFRACTIONf_plane_restr0.007329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.6330.25741010.25851892X-RAY DIFFRACTION69
1.633-1.6810.2703970.22482237X-RAY DIFFRACTION81
1.681-1.73530.23781260.20652501X-RAY DIFFRACTION92
1.7353-1.79730.1861520.17742725X-RAY DIFFRACTION99
1.7973-1.86930.18791420.15852723X-RAY DIFFRACTION99
1.8693-1.95440.18951330.1512698X-RAY DIFFRACTION99
1.9544-2.05740.17481440.14872725X-RAY DIFFRACTION99
2.0574-2.18630.16881330.1382743X-RAY DIFFRACTION100
2.1863-2.35510.15351390.13592696X-RAY DIFFRACTION99
2.3551-2.59210.16511690.1462674X-RAY DIFFRACTION99
2.5921-2.96710.20221540.15252705X-RAY DIFFRACTION99
2.9671-3.73810.14811440.14152722X-RAY DIFFRACTION99
3.7381-48.12070.13081500.12892679X-RAY DIFFRACTION99

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