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- PDB-5llk: Crystal structure of human alpha-dystroglycan -

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Basic information

Entry
Database: PDB / ID: 5llk
TitleCrystal structure of human alpha-dystroglycan
ComponentsDystroglycan
KeywordsCELL ADHESION / Dystroglycan / Extraellular Matrix Adhesion
Function / homology
Function and homology information


Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / regulation of embryonic cell shape / O-linked glycosylation ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / regulation of embryonic cell shape / O-linked glycosylation / 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 / photoreceptor ribbon synapse / dystroglycan binding / cellular response to cholesterol / nerve development / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / 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 / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / laminin binding / 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 / Regulation of expression of SLITs and ROBOs / Golgi lumen / cellular response to mechanical stimulus / protein transport / virus receptor activity / lamellipodium / actin binding / postsynaptic membrane / basolateral plasma membrane / collagen-containing extracellular matrix / cytoskeleton / external side of plasma membrane / endoplasmic reticulum lumen / focal adhesion / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCovaceuszach, S. / Cassetta, A. / Lamba, D. / Brancaccio, A. / Bozzi, M. / Sciandra, F. / Bigotti, M.G. / Konarev, P.V.
CitationJournal: FEBS Open Bio / Year: 2017
Title: Structural flexibility of human alpha-dystroglycan.
Authors: Covaceuszach, S. / Bozzi, M. / Bigotti, M.G. / Sciandra, F. / Konarev, P.V. / Brancaccio, A. / Cassetta, A.
History
DepositionJul 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6793
Polymers28,5541
Non-polymers1242
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint6 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.520, 71.520, 144.010
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-616-

HOH

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Components

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


Mass: 28554.453 Da / Num. of mol.: 1 / Fragment: UNP residues 52-315 / Mutation: R168H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAG1 / Organ: Skeletal Muscle / Plasmid: pHis-Trx / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14118
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.8 M Sodium Citrate / PH range: 6.8-7.2

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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: Jan 22, 2016 / Details: Pt-coated mirror
RadiationMonochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48 Å / Num. obs: 25220 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 21.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.61 / CC1/2: 0.868 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2328: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U2C

1u2c


Resolution: 1.8→35.76 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 24.21
Details: Refined: Bulk Solvent + coordinates + TLS + ADP + occupancies Refinement Target: ML TLS refinement: 6 groups Occupancies: selected residues with low electron density
RfactorNum. reflection% reflection
Rfree0.1947 1258 5 %
Rwork0.1633 --
obs0.1649 25153 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 8 129 1839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011747
X-RAY DIFFRACTIONf_angle_d1.0122377
X-RAY DIFFRACTIONf_dihedral_angle_d17.8991051
X-RAY DIFFRACTIONf_chiral_restr0.063277
X-RAY DIFFRACTIONf_plane_restr0.007305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.87210.36451340.37012523X-RAY DIFFRACTION94
1.8721-1.95730.29841380.24872622X-RAY DIFFRACTION98
1.9573-2.06050.27771400.20152667X-RAY DIFFRACTION99
2.0605-2.18960.19271400.18382681X-RAY DIFFRACTION100
2.1896-2.35860.19531410.17062672X-RAY DIFFRACTION100
2.3586-2.59590.21881400.17712673X-RAY DIFFRACTION99
2.5959-2.97140.22971420.17662679X-RAY DIFFRACTION100
2.9714-3.7430.17871420.15352698X-RAY DIFFRACTION100
3.743-35.7670.15671410.13272680X-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)
11.45110.27730.43541.20590.12721.6474-0.0096-0.0661-0.3679-0.0374-0.1813-0.22860.43060.27140.00020.4999-0.0777-0.04290.41430.03220.4416-20.9156-13.968238.0541
20.96560.0302-0.67080.83430.44011.03380.04790.0254-0.181-0.0593-0.2874-0.0730.02320.42170.0010.388-0.0462-0.05490.3016-0.01260.36-26.1584-11.416139.4008
30.493-0.19950.7350.1944-0.00381.8464-0.0788-0.12060.11240.1731-0.1001-0.0614-0.50430.0623-0.08570.4632-0.11-0.04220.34640.01050.3416-23.8242-3.21125.7148
40.28730.10820.13930.38850.31470.31250.2509-0.3606-0.01170.4518-0.0815-0.13580.3294-0.09420.00030.4038-0.0209-0.04290.28480.0220.3176-26.2663-13.489917.5766
52.48570.70240.0662.8537-0.60793.14270.02510.07370.123-0.0823-0.081-0.1171-0.19460.17-0.00010.2608-0.0018-0.00870.20820.03390.263-27.7025-4.43327.6753
60.8071-0.60530.03620.46140.02230.33110.303-0.27330.35310.2097-0.3537-0.1587-0.56960.25650.01350.4063-0.0936-0.0090.26060.03380.321-26.53280.98067.1826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 203 )
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 218 )
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 292 )
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 304 )

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