+Open data
-Basic information
Entry | Database: PDB / ID: 2rot | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of chimeric variant of SH3 domain- SHH | ||||||
Components | Spectrin alpha chain, brain | ||||||
Keywords | PROTEIN BINDING / SH3 / chimeric protein / alpha-spectrin / Actin capping / Actin-binding / Calcium / Calmodulin-binding / Cytoplasm / Cytoskeleton / Phosphoprotein / SH3 domain | ||||||
Function / homology | Function and homology information costamere / actin filament capping / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | SHH was constructed on the basis of alpa-spectrin wild type SH3-domain, containing 10 extra ...SHH was constructed on the basis of alpa-spectrin wild type SH3-domain, containing 10 extra residues placed between 45th and 48th polypeptides' residues. Insertion of beta sheet includes 48-56 residues (KITVNGKTYE) between 45-48 of SH3-pwt (1SHG) | ||||||
Authors | Kutyshenko, N.P. / Prokhorov, D.A. / Timchenko, M.A. / Kudrevatykh, Y.A. / Gushchina, L.V. / Khristoforov, V.S. / Filimonov, V.V. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2009 Title: Solution structure and dynamics of the chimeric SH3 domains, SHH- and SHA-"Bergeracs". Authors: Kutyshenko, V.P. / Prokhorov, D.A. / Timchenko, M.A. / Kudrevatykh, Y.A. / Gushchina, L.V. / Khristoforov, V.S. / Filimonov, V.V. / Uversky, V.N. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: Different folding transition states may result in the same native structure. Authors: Viguera, A.R. / Serrano, L. / Wilmanns, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2rot.cif.gz | 446.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2rot.ent.gz | 378.3 KB | Display | PDB format |
PDBx/mmJSON format | 2rot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/2rot ftp://data.pdbj.org/pub/pdb/validation_reports/ro/2rot | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 8136.353 Da / Num. of mol.: 1 / Fragment: ALPHA-SPECTRIN SH3 Domain Source method: isolated from a genetically manipulated source Details: INSERTION OF BETA SHEET INCLUDING 47-56 RESIDUES (KITVNGKTYE) BETWEEN 47-48 OF SH3-PWT (1SHG). Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07751 |
---|---|
Sequence details | INSERTION OF BETA SHEET INCLUDING 47-56 RESIDUES (KITVNGKTYE |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: SHH was constructed on the basis of alpa-spectrin wild type SH3-domain, containing 10 extra residues placed between 45th and 48th polypeptides' residues. Insertion of beta sheet includes 48- ...Details: SHH was constructed on the basis of alpa-spectrin wild type SH3-domain, containing 10 extra residues placed between 45th and 48th polypeptides' residues. Insertion of beta sheet includes 48-56 residues (KITVNGKTYE) between 45-48 of SH3-pwt (1SHG) | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||||||||||||||
NMR details | Text: The structure was determined using dihedral angles PHI and PSI predicted by program TALOS. H-bonds were determined on the basis of temperature dependence of NH chemical shifts |
-Sample preparation
Details | Contents: 2.5mM [U-98% 13C; U-98% 15N] alpha-spectrin SHH, 90% H2O, 10% [U-99% 2H] D2O, 25mM [U-99% 2H] sodium acetate, 0.03% sodium azide, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||
Sample conditions | Ionic strength: 20 / pH: 3.5 / Pressure: 74 3 / Temperature: 299 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1156 / NOE intraresidue total count: 268 / NOE long range total count: 402 / NOE medium range total count: 134 / NOE sequential total count: 352 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.24 Å | ||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0041 Å / Distance rms dev error: 0.0011 Å |