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- PDB-9d58: Human Dystrophin tandem calponin homology actin-binding domain cr... -

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Basic information

Entry
Database: PDB / ID: 9d58
TitleHuman Dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation
ComponentsDystrophin
KeywordsSTRUCTURAL PROTEIN / Actin-binding domain / tandem calponin homology domain / Dystrophin / Duchenne Muscular Dystrophy / DMD / Cytoskeleton
Function / homology
Function and homology information


regulation of muscle system process / regulation of cellular response to growth factor stimulus / syntrophin complex / cardiac muscle cell action potential / regulation of skeletal muscle contraction / synaptic signaling / dystrophin-associated glycoprotein complex / cell-substrate junction / peptide biosynthetic process / motile cilium assembly ...regulation of muscle system process / regulation of cellular response to growth factor stimulus / syntrophin complex / cardiac muscle cell action potential / regulation of skeletal muscle contraction / synaptic signaling / dystrophin-associated glycoprotein complex / cell-substrate junction / peptide biosynthetic process / motile cilium assembly / dystroglycan binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / vinculin binding / regulation of sodium ion transmembrane transport / Formation of the dystrophin-glycoprotein complex (DGC) / costamere / muscle cell development / regulation of calcium ion transmembrane transport / neuron projection terminus / Striated Muscle Contraction / filopodium membrane / structural constituent of muscle / muscle organ development / muscle cell cellular homeostasis / myosin binding / maintenance of blood-brain barrier / 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 / skeletal muscle tissue development / cardiac muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle stretch / positive regulation of neuron differentiation / regulation of heart rate / filopodium / positive regulation of neuron projection development / sarcolemma / structural constituent of cytoskeleton / Z disc / intracellular protein localization / 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
Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / : / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. ...Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / : / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsStreeter, O. / Shi, K. / Ervasti, J.M. / Evans III, R.L. / Muretta, J.M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Human dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation.
Authors: Streeter, O. / Shi, K. / Vavra, J. / Aihara, H. / Ervasti, J.M. / Evans 3rd, R. / Muretta, J.M.
History
DepositionAug 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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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)114,2934
Polymers114,2934
Non-polymers00
Water4,306239
1
A: Dystrophin


Theoretical massNumber of molelcules
Total (without water)28,5731
Polymers28,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dystrophin


Theoretical massNumber of molelcules
Total (without water)28,5731
Polymers28,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dystrophin


Theoretical massNumber of molelcules
Total (without water)28,5731
Polymers28,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dystrophin


Theoretical massNumber of molelcules
Total (without water)28,5731
Polymers28,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.774, 143.138, 59.862
Angle α, β, γ (deg.)90.000, 102.210, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 16 through 19 or (resid 20...
d_2ens_1(chain "B" and (resid 16 through 69 or (resid 70...
d_3ens_1(chain "C" and (resid 16 through 19 or (resid 20...
d_4ens_1(chain "D" and (resid 16 through 19 or (resid 20...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUARGARGAA16 - 14716 - 147
d_12SERSERGLNGLNAA149 - 243149 - 243
d_21GLUGLUARGARGBB16 - 14716 - 147
d_22SERSERGLNGLNBB149 - 243149 - 243
d_31GLUGLUARGARGCC16 - 14716 - 147
d_32SERSERGLNGLNCC149 - 243149 - 243
d_41GLUGLUARGARGDD16 - 14716 - 147
d_42SERSERGLNGLNDD149 - 243149 - 243

NCS oper:
IDCodeMatrixVector
1given(0.204993715815, 0.00192136231542, -0.978761403429), (0.0130608108891, -0.999914405495, 0.000772595134726), (-0.978676142396, -0.0129417947432, -0.205001264029)33.4736860333, 100.78986266, 21.5809868621
2given(-0.999997896084, 0.00142426008817, -0.00147624891391), (0.00141952730711, 0.999993865872, 0.00320205555456), (0.00148080041834, 0.00319995324206, -0.999993783745)39.6288434478, -0.136559627654, 69.1733466971
3given(-0.207312979784, -0.00569433738494, 0.978258096279), (0.0131961353515, -0.999908355035, -0.00302382918935), (0.978185662553, 0.0122823472076, 0.20736912384)21.3483521848, 100.926686402, 26.0976578323

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Components

#1: Protein
Dystrophin


Mass: 28573.312 Da / Num. of mol.: 4
Fragment: actin-binding domain/calponin homology domains 1 and 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMD / Production host: Escherichia coli (E. coli) / References: UniProt: P11532
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.7, 30% w/v Polyethylene monomethyl ether (MPEG) 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.94→58.51 Å / Num. obs: 70503 / % possible obs: 97.9 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.069 / Rrim(I) all: 0.126 / Rsym value: 0.104 / Net I/σ(I): 7.1
Reflection shellResolution: 1.94→1.978 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3535 / CC1/2: 0.838 / Rpim(I) all: 0.322 / Rrim(I) all: 0.58 / Rsym value: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→58.51 Å / Cross valid method: FREE R-VALUE / σ(F): 20.53 / Phase error: 39.8923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2617 3575 5.07 %
Rwork0.2157 66885 -
obs0.2407 70460 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.13 Å2
Refinement stepCycle: LAST / Resolution: 1.94→58.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7233 0 0 239 7472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00367386
X-RAY DIFFRACTIONf_angle_d0.6410054
X-RAY DIFFRACTIONf_chiral_restr0.04261172
X-RAY DIFFRACTIONf_plane_restr0.00441283
X-RAY DIFFRACTIONf_dihedral_angle_d6.0334979
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.498290006142
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.359649290079
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.468632507504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.34861630.29823367X-RAY DIFFRACTION93.84
1.98-2.010.37551560.28663315X-RAY DIFFRACTION92.99
2.01-2.050.30531780.29083311X-RAY DIFFRACTION92.05
2.05-2.090.32431420.283394X-RAY DIFFRACTION94.17
2.09-2.140.34772100.28233334X-RAY DIFFRACTION92.23
2.14-2.190.31761960.27983335X-RAY DIFFRACTION93.5
2.19-2.240.2711850.27583339X-RAY DIFFRACTION92.98
2.24-2.30.30171660.26423403X-RAY DIFFRACTION93.77
2.3-2.370.34641980.27163311X-RAY DIFFRACTION93.11
2.37-2.450.31991740.26083384X-RAY DIFFRACTION93.53
2.45-2.540.27591640.25593344X-RAY DIFFRACTION93.46
2.54-2.640.32491600.24833375X-RAY DIFFRACTION93.91
2.64-2.760.31111670.25443394X-RAY DIFFRACTION93.76
2.76-2.90.30592050.24883335X-RAY DIFFRACTION92.56
2.9-3.090.34711460.24063384X-RAY DIFFRACTION94.21
3.09-3.320.291800.22873365X-RAY DIFFRACTION92.39
3.32-3.660.32551760.20373259X-RAY DIFFRACTION91.19
3.66-4.190.22251750.18923219X-RAY DIFFRACTION88.78
4.19-5.280.20511820.17883384X-RAY DIFFRACTION93.69
5.28-58.510.26421640.23323421X-RAY DIFFRACTION92.94

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