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- PDB-1u2c: Crystal Structure of a-dystroglycan -

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Basic information

Entry
Database: PDB / ID: 1u2c
TitleCrystal Structure of a-dystroglycan
ComponentsDystroglycan
KeywordsPROTEIN BINDING / IG-like domain / S6 like fold
Function / homology
Function and homology information


O-linked glycosylation / dystroglycan complex / nerve maturation / muscle attachment / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / Regulation of expression of SLITs and ROBOs / contractile ring / regulation of gastrulation / calcium-dependent cell-matrix adhesion ...O-linked glycosylation / dystroglycan complex / nerve maturation / muscle attachment / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / Regulation of expression of SLITs and ROBOs / contractile ring / regulation of gastrulation / calcium-dependent cell-matrix adhesion / microtubule anchoring / 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 / dystroglycan binding / nerve development / cellular response to cholesterol / photoreceptor ribbon synapse / vinculin binding / myelination in peripheral nervous system / branching involved in salivary gland morphogenesis / node of Ranvier / costamere / skeletal muscle tissue regeneration / angiogenesis involved in wound healing / commissural neuron axon guidance / response to muscle activity / axon regeneration / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / structural constituent of muscle / positive regulation of cell-matrix adhesion / postsynaptic cytosol / 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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of MAPK cascade / Schwann cell development / heart morphogenesis / GABA-ergic synapse / laminin binding / tubulin binding / SH2 domain 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 / lamellipodium / virus receptor activity / heart development / actin binding / basolateral plasma membrane / postsynaptic membrane / postsynapse / 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 / MIR / Resolution: 2.3 Å
AuthorsBozic, D. / Sciandra, F. / Lamba, D. / Brancaccio, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Structure of the N-terminal Region of Murine Skeletal Muscle {alpha}-Dystroglycan Discloses a Modular Architecture
Authors: Bozic, D. / Sciandra, F. / Lamba, D. / Brancaccio, A.
History
DepositionJul 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)26,2271
Polymers26,2271
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.445, 71.445, 144.233
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Dystroglycan / alpha-dystroglycan


Mass: 26226.779 Da / Num. of mol.: 1 / Fragment: residues 58-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q62165
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.46 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→35.72 Å / Num. all: 11584 / Num. obs: 11584 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 29 Å2
Reflection shellHighest resolution: 2.3 Å / % possible all: 94.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→35.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 259321.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1195 10.3 %RANDOM
Rwork0.208 ---
obs0.208 11584 94.8 %-
all-11584 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.5021 Å2 / ksol: 0.32933 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.54 Å26.17 Å20 Å2
2--6.54 Å20 Å2
3----13.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 0 199 1905
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 194 10.6 %
Rwork0.238 1628 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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