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- PDB-1eg3: STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BE... -

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Basic information

Entry
Database: PDB / ID: 1eg3
TitleSTRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BETA-DYSTROGLYCAN PEPTIDE
ComponentsDYSTROPHIN
KeywordsSTRUCTURAL PROTEIN / EF-hand like domain / WW domain
Function / homology
Function and homology information


regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / synaptic signaling / cardiac muscle cell action potential / regulation of voltage-gated calcium channel activity / negative regulation of peptidyl-cysteine S-nitrosylation / positive regulation of sodium ion transmembrane transporter activity / dystrophin-associated glycoprotein complex ...regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / synaptic signaling / cardiac muscle cell action potential / regulation of voltage-gated calcium channel activity / negative regulation of peptidyl-cysteine S-nitrosylation / positive regulation of sodium ion transmembrane transporter activity / dystrophin-associated glycoprotein complex / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / peptide biosynthetic process / cell-substrate junction / motile cilium assembly / dystroglycan binding / vinculin binding / muscle cell development / costamere / neuron projection terminus / Striated Muscle Contraction / filopodium membrane / muscle organ development / structural constituent of muscle / muscle cell cellular homeostasis / myosin binding / maintenance of blood-brain barrier / nitric-oxide synthase binding / negative regulation of peptidyl-serine phosphorylation / Non-integrin membrane-ECM interactions / neuron development / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / skeletal muscle tissue development / regulation of ryanodine-sensitive calcium-release channel activity / response to muscle stretch / positive regulation of neuron differentiation / regulation of heart rate / filopodium / protein localization / structural constituent of cytoskeleton / sarcolemma / positive regulation of neuron projection development / Z disc / actin binding / protein-containing complex assembly / postsynaptic membrane / cytoskeleton / membrane raft / synapse / cell surface / protein-containing complex / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #70 / 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 ...Helix Hairpins - #70 / 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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Calponin homology (CH) domain / 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. / WW domain / Helix Hairpins / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / EF-hand / Recoverin; domain 1 / Single Sheet / Helix non-globular / Special / EF-hand domain pair / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
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

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Assembly

Deposited unit
A: DYSTROPHIN


Theoretical massNumber of molelcules
Total (without water)29,8451
Polymers29,8451
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.710, 67.470, 85.490
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 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, glycerol, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMMOPS1drop
3100 mM1dropNaCl
45 mMdithiothreitol1drop
5100 mMMOPS1reservoir
61.0 Mammonium sulfate1reservoir
710 %(v/v)glycerol1reservoir
85 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 213 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.922
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.922 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 144120 / Num. obs: 19962 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.347 / Num. unique all: 1929 / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 144120

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 998 -RANDOM
Rwork0.194 ---
all-20123 --
obs-19962 99.2 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 0 266 2355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.563
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: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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