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- PDB-1dxx: N-terminal Actin-binding Domain of Human Dystrophin -

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Basic information

Entry
Database: PDB / ID: 1dxx
TitleN-terminal Actin-binding Domain of Human Dystrophin
ComponentsDYSTROPHIN
KeywordsSTRUCTURAL PROTEIN / DYSTROPHIN / MUSCULAR DYSTROPHY / CALPONIN HOMOLOGY DOMAIN / ACTIN-BINDING / UTROPHIN
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 / maintenance of blood-brain barrier / myosin binding / nitric-oxide synthase binding / Non-integrin membrane-ECM interactions / neuron development / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / negative regulation of peptidyl-serine phosphorylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / skeletal muscle tissue development / regulation of ryanodine-sensitive calcium-release channel activity / cardiac muscle contraction / response to muscle stretch / positive regulation of neuron differentiation / regulation of heart rate / filopodium / sarcolemma / protein localization / structural constituent of cytoskeleton / positive regulation of neuron projection development / Z disc / actin binding / postsynaptic membrane / protein-containing complex assembly / cytoskeleton / membrane raft / synapse / cell surface / protein-containing complex / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. ...Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / 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. / 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 domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNorwood, F.L. / Sutherland-Smith, A.J. / Keep, N.H. / Kendrick-Jones, J.
CitationJournal: Structure / Year: 2000
Title: The Structure of the N-Terminal Actin-Binding Domain of Human Dystrophin and How Mutations in This Domain May Cause Duchenne or Becker Muscular Dystrophy
Authors: Norwood, F.L. / Sutherland-Smith, A.J. / Keep, N.H. / Kendrick-Jones, J.
History
DepositionJan 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEET IN EACH DIMERIC MOLECULE INVOLVES A STRAND CONTRIBUTED ... SHEET DETERMINATION METHOD: DSSP THE SHEET IN EACH DIMERIC MOLECULE INVOLVES A STRAND CONTRIBUTED FROM EACH COMPONENT CHAIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DYSTROPHIN
B: DYSTROPHIN
C: DYSTROPHIN
D: DYSTROPHIN


Theoretical massNumber of molelcules
Total (without water)113,8374
Polymers113,8374
Non-polymers00
Water1,33374
1
A: DYSTROPHIN
B: DYSTROPHIN


Theoretical massNumber of molelcules
Total (without water)56,9192
Polymers56,9192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-34.2 kcal/mol
Surface area25390 Å2
MethodPQS
2
C: DYSTROPHIN
D: DYSTROPHIN


Theoretical massNumber of molelcules
Total (without water)56,9192
Polymers56,9192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-32.6 kcal/mol
Surface area25340 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.690, 79.330, 81.950
Angle α, β, γ (deg.)61.08, 78.22, 70.54
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.77329, 0.63406, 0.00062), (0.63405, 0.77329, -0.00222), (-0.00189, -0.00133, -1)25.70045, -9.12847, 38.25601
2given(0.76917, -0.63162, -0.09712), (-0.63138, -0.77459, 0.0371), (-0.09866, 0.03278, -0.99458)13.40925, 31.93406, 39.52884
3given(-0.99518, 0.00171, 0.09803), (-0.00512, -0.99939, -0.03453), (0.09792, -0.03487, 0.99458)35.38485, 24.2005, -1.41113

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Components

#1: Protein
DYSTROPHIN /


Mass: 28459.275 Da / Num. of mol.: 4 / Fragment: ACTIN-BINDING / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLESkeletal muscle / Cellular location: CELL MEMBRANE / Gene: DMD / Plasmid: PGEX-4T2 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11532
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL FRAGMENT 1-246

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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: 2.8 Å3/Da / Density % sol: 52 % / Description: DOMAIN SWAPPED SEARCH MODEL USED
Crystal growpH: 7.4 / Details: 1.55M AMMONIUM FORMATE, 0.1M HEPES 7.4, pH 7.40
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.55 Mammonium formate1drop
30.1 MHEPES1drop
41.55 Mammonium formate1reservoir
50.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 36284 / % possible obs: 95.4 % / Redundancy: 1.7 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.6 / % possible all: 91.6
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 91.6 % / Num. unique obs: 3448

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAG

1qag


Resolution: 2.6→20 Å / SU B: 5.77 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.86 / ESU R Free: 0.34
Details: XPLOR BULK SOLVENT MODEL USED TERMINAL RESIDUES FROM PGEX-4T2 CLONING SITE WERE NOT OBSERVED IN MAPS. TIGHT NCS RESTRAINTS WERE IMPOSED DURING ALL STAGES OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1767 5 %RANDOM
Rwork0.232 ---
obs-34446 95 %-
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-8.28 Å2-0.55 Å2-1.07 Å2
2---3.92 Å2-0.5 Å2
3----4.32 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7548 0 0 74 7622
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.016
X-RAY DIFFRACTIONp_angle_d0.0430.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.82.6
X-RAY DIFFRACTIONp_mcangle_it4.34
X-RAY DIFFRACTIONp_scbond_it4.13.8
X-RAY DIFFRACTIONp_scangle_it5.14
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd0.210.3
X-RAY DIFFRACTIONp_multtor_nbd0.270.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.190.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor1815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor obs: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å / Rfactor Rfree: 0.314 / Rfactor obs: 0.265

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