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- PDB-5n4h: Crystal structure of the D109N mutant of the mouse alpha-Dystrogl... -

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Basic information

Entry
Database: PDB / ID: 5n4h
TitleCrystal structure of the D109N mutant of the mouse alpha-Dystroglycan N-terminal region
ComponentsDystroglycan
KeywordsCELL ADHESION / Dystroglycan / Laminin Binding
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 / contractile ring / Regulation of expression of SLITs and ROBOs / 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 / contractile ring / Regulation of expression of SLITs and ROBOs / 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 / photoreceptor ribbon synapse / dystroglycan binding / cellular response to cholesterol / nerve development / vinculin binding / myelination in peripheral nervous system / branching involved in salivary gland morphogenesis / node of Ranvier / costamere / commissural neuron axon guidance / angiogenesis involved in wound healing / response to muscle activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic cytosol / axon regeneration / structural constituent of muscle / positive regulation of cell-matrix adhesion / epithelial tube branching involved in lung morphogenesis / positive regulation of oligodendrocyte differentiation / regulation of synapse organization / negative regulation of MAPK cascade / alpha-actinin binding / plasma membrane raft / membrane protein ectodomain proteolysis / cellular response to organic cyclic compound / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / laminin binding / Schwann cell development / heart morphogenesis / SH2 domain binding / tubulin binding / nuclear periphery / negative regulation of cell migration / filopodium / axon guidance / morphogenesis of an epithelium / adherens junction / regulation of synaptic plasticity / sarcolemma / response to peptide hormone / cellular response to mechanical stimulus / cell-cell junction / protein transport / virus receptor activity / lamellipodium / actin binding / heart development / postsynapse / postsynaptic membrane / basolateral plasma membrane / cytoskeleton / membrane raft / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / protein-containing complex binding / cell surface / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytoplasm
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
DI(HYDROXYETHYL)ETHER / Dystroglycan 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsCassetta, A. / Covaceuszach, S. / Brancaccio, A. / Sciandra, F. / Bozzi, M. / Bigotti, M.G. / Konarev, P.V.
Funding support United Kingdom, France, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Telethon France
CitationJournal: PLoS ONE / Year: 2017
Title: The effect of the pathological V72I, D109N and T190M missense mutations on the molecular structure of alpha-dystroglycan.
Authors: Covaceuszach, S. / Bozzi, M. / Bigotti, M.G. / Sciandra, F. / Konarev, P.V. / Brancaccio, A. / Cassetta, A.
History
DepositionFeb 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5794
Polymers28,3481
Non-polymers2303
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint9 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.740, 71.740, 143.990
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-651-

HOH

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Components

#1: Protein Dystroglycan / / Dystrophin-associated glycoprotein 1


Mass: 28348.291 Da / Num. of mol.: 1 / Mutation: D109N, R166H
Source method: isolated from a genetically manipulated source
Details: DG hypoglycosylated mutant / Source: (gene. exp.) Mus musculus (house mouse) / Tissue: Skeletal Muscle / Gene: Dag1, Dag-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q62165
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.7 M Citrate Buffer, pH 7.0 5.5 mg/mL protein in 25 mM Tris, 150 mM NaCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2016 / Details: Toroidal Pt-coated mirror
RadiationMonochromator: Double Crystal Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→48 Å / Num. obs: 30354 / % possible obs: 99.7 % / Redundancy: 7.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.103 / Net I/σ(I): 11.96
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.098 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 2776 / CC1/2: 0.833 / Rrim(I) all: 1.181 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.11_2561)refinement
XDSVERSION OCT 15, 2015data reduction
XSCALEVERSION OCT 15, 2015data scaling
PHASER2.7.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U2C

1u2c


Resolution: 1.701→47.997 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 19.93
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 1516 5 %Random Selection
Rwork0.1591 ---
obs0.1603 30317 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.701→47.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 15 196 1951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131820
X-RAY DIFFRACTIONf_angle_d1.272479
X-RAY DIFFRACTIONf_dihedral_angle_d18.8031103
X-RAY DIFFRACTIONf_chiral_restr0.076285
X-RAY DIFFRACTIONf_plane_restr0.009323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7011-1.7560.35521380.35312619X-RAY DIFFRACTION99
1.756-1.81870.31241360.26842584X-RAY DIFFRACTION99
1.8187-1.89160.19941380.20432629X-RAY DIFFRACTION99
1.8916-1.97760.20351370.17332605X-RAY DIFFRACTION100
1.9776-2.08190.17941380.16442627X-RAY DIFFRACTION100
2.0819-2.21230.18541380.15542626X-RAY DIFFRACTION100
2.2123-2.38320.16441380.14652612X-RAY DIFFRACTION100
2.3832-2.6230.19581380.15682618X-RAY DIFFRACTION100
2.623-3.00250.16781390.15682638X-RAY DIFFRACTION100
3.0025-3.78260.16531380.14942624X-RAY DIFFRACTION100
3.7826-48.01580.17431380.14092619X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1187-0.05940.10631.0358-0.28591.5892-0.0520.2267-0.0877-0.0288-0.0382-0.0990.2384-0.073-0.00050.2578-0.0031-0.00730.3517-0.04020.2625-13.6646-7.3195-38.5957
20.0503-0.0892-0.04340.30.10710.16170.14650.79380.0578-0.8115-0.2320.2257-0.1238-0.54030.00050.5923-0.04940.02181.1133-0.19070.6073-32.9245-4.9295-14.9941
32.00990.0825-0.39991.19750.08092.451-0.04540.02980.00290.0394-0.02730.085-0.0045-0.2118-0.01170.1460.00610.00850.184-0.01730.1698-17.14950.7233-9.1908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 156)
2X-RAY DIFFRACTION2chain 'A' and (resid 157 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 303 )

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