[English] 日本語
![](img/lk-miru.gif)
- PDB-3d2s: Crystal structure of MBNL1 tandem zinc finger 3 and 4 domain in c... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3d2s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MBNL1 tandem zinc finger 3 and 4 domain in complex with CGCUGU RNA | ||||||
![]() |
| ||||||
![]() | METAL BINDING PROTEIN/RNA / tandem zinc finger domain / RNA / Metal-binding / Nucleus / RNA-binding / Zinc-finger / METAL BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | ![]() regulatory region RNA binding / myoblast differentiation / embryonic limb morphogenesis / regulation of RNA splicing / RNA splicing / mRNA processing / cytoplasmic stress granule / double-stranded RNA binding / nervous system development / in utero embryonic development ...regulatory region RNA binding / myoblast differentiation / embryonic limb morphogenesis / regulation of RNA splicing / RNA splicing / mRNA processing / cytoplasmic stress granule / double-stranded RNA binding / nervous system development / in utero embryonic development / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() Synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Teplova, M. / Patel, D.J. | ||||||
![]() | ![]() Title: Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1. Authors: Teplova, M. / Patel, D.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 87.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 65.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 502.3 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 1868.149 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized RNA oligonucleotide / Source: (synth.) Synthetic construct (others) #2: Protein | Mass: 8169.182 Da / Num. of mol.: 4 Fragment: tandem zinc finger 3 and 4 domains (UNP residues 178-246) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.18 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.5 Details: 25% PEG 3350, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, temperature 277K | ||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 38651 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Rsym value: 0.074 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 3846 / Rsym value: 0.44 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: MBNL1 ZnF3/4 structure Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.62 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.101 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.698→1.742 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 13.995 Å / Origin y: 3.97 Å / Origin z: 13.604 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|