+Open data
-Basic information
Entry | Database: PDB / ID: 1dxx | ||||||
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Title | N-terminal Actin-binding Domain of Human Dystrophin | ||||||
Components | DYSTROPHIN | ||||||
Keywords | STRUCTURAL 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 / 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 | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Norwood, F.L. / Sutherland-Smith, A.J. / Keep, N.H. / Kendrick-Jones, J. | ||||||
Citation | Journal: 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 |
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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dxx.cif.gz | 195.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dxx.ent.gz | 156.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dxx_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 1dxx_full_validation.pdf.gz | 504 KB | Display | |
Data in XML | 1dxx_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 1dxx_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dxx ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dxx | HTTPS FTP |
-Related structure data
Related structure data | 1qagS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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: 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 / | Sequence details | N-TERMINAL FRAGMENT 1-246 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 52 % / Description: DOMAIN SWAPPED SEARCH MODEL USED | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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.
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Displacement parameters | Biso mean: 37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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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 |