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- PDB-1eg4: STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BE... -

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Basic information

Entry
Database: PDB / ID: 1eg4
TitleSTRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BETA-DYSTROGLYCAN PEPTIDE
Components
  • BETA-DYSTROGLYCAN
  • DYSTROPHIN
KeywordsSTRUCTURAL PROTEIN / EF-hand like domain / WW domain / Polyproline type II (PPII) helix
Function / homology
Function and homology information


Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / muscle attachment / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / regulation of embryonic cell shape / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / regulation of muscle system process ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / muscle attachment / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / regulation of embryonic cell shape / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / regulation of muscle system process / O-linked glycosylation / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / negative regulation of peptidyl-cysteine S-nitrosylation / contractile ring / regulation of voltage-gated calcium channel activity / synaptic signaling / regulation of gastrulation / cardiac muscle cell action potential / calcium-dependent cell-matrix adhesion / morphogenesis of an epithelial sheet / dystrophin-associated glycoprotein complex / positive regulation of sodium ion transmembrane transporter activity / microtubule anchoring / laminin-1 binding / response to denervation involved in regulation of muscle adaptation / cell-substrate junction / motile cilium assembly / peptide biosynthetic process / positive regulation of myelination / basement membrane organization / photoreceptor ribbon synapse / nerve development / dystroglycan binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cellular response to cholesterol / Formation of the dystrophin-glycoprotein complex (DGC) / vinculin binding / regulation of epithelial to mesenchymal transition / EGR2 and SOX10-mediated initiation of Schwann cell myelination / myelination in peripheral nervous system / branching involved in salivary gland morphogenesis / skeletal muscle tissue regeneration / costamere / commissural neuron axon guidance / muscle cell development / neuron projection terminus / node of Ranvier / Striated Muscle Contraction / angiogenesis involved in wound healing / filopodium membrane / axon regeneration / structural constituent of muscle / positive regulation of cell-matrix adhesion / muscle cell cellular homeostasis / nitric-oxide synthase binding / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / muscle organ development / response to muscle activity / epithelial tube branching involved in lung morphogenesis / regulation of synapse organization / myosin binding / maintenance of blood-brain barrier / alpha-actinin binding / membrane protein ectodomain proteolysis / basement membrane / positive regulation of oligodendrocyte differentiation / Non-integrin membrane-ECM interactions / postsynaptic cytosol / regulation of ryanodine-sensitive calcium-release channel activity / plasma membrane raft / ECM proteoglycans / negative regulation of MAPK cascade / neuron development / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / heart morphogenesis / skeletal muscle tissue development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / laminin binding / response to muscle stretch / positive regulation of neuron differentiation / tubulin binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / SH2 domain binding / nuclear periphery / regulation of heart rate / axon guidance / negative regulation of cell migration / morphogenesis of an epithelium / GABA-ergic synapse / filopodium / adherens junction / sarcolemma / regulation of synaptic plasticity / positive regulation of neuron projection development / structural constituent of cytoskeleton / response to peptide hormone / Z disc
Similarity search - Function
Helix Hairpins - #70 / 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. ...Helix Hairpins - #70 / 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 / Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / : / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Cadherin-like superfamily / Calponin homology domain / Zinc finger ZZ-type signature. / Calponin homology (CH) domain / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Helix Hairpins / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / EF-hand / Single Sheet / Recoverin; domain 1 / Helix non-globular / Special / EF-hand domain pair / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Dystrophin / Dystroglycan 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHuang, X. / Poy, F. / Zhang, R. / Joachimiak, A. / Sudol, M. / Eck, M.J.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of a WW domain containing fragment of dystrophin in complex with beta-dystroglycan.
Authors: Huang, X. / Poy, F. / Zhang, R. / Joachimiak, A. / Sudol, M. / Eck, M.J.
History
DepositionFeb 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
P: BETA-DYSTROGLYCAN
A: DYSTROPHIN


Theoretical massNumber of molelcules
Total (without water)31,5912
Polymers31,5912
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.680, 67.050, 83.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide BETA-DYSTROGLYCAN


Mass: 1746.036 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized and occurs naturally in Homo Sapiens (Human)
References: UniProt: Q14118
#2: Protein DYSTROPHIN


Mass: 29845.232 Da / Num. of mol.: 1 / Fragment: WW DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2TK / Production host: Escherichia coli (E. coli) / References: UniProt: P11532
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, glycerol, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMMOPS1drop
3100 mM1dropNaCl
45 mMdithiothreitol1drop
5100 mMHEPES1reservoir
61.0 Mammonium sulfate1reservoir
710 %(v/v)glycerol1reservoir
85 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 213 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07
DetectorType: APS-1 / Detector: CCD / Date: Apr 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 120237 / Num. obs: 21895 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5 % / Rmerge(I) obs: 0.295 / Num. unique all: 2146 / % possible all: 95.3
Reflection
*PLUS
Num. measured all: 120237

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Processing

Software
NameVersionClassification
DMmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementResolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1095 -RANDOM
Rwork0.197 ---
all-22274 --
obs-21895 98.3 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 0 283 2478
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.654
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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