+
Open data
-
Basic information
Entry | Database: PDB / ID: 4b8a | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of yeast NOT1 MIF4G domain co-crystallized with CAF1 | |||||||||
![]() |
| |||||||||
![]() | TRANSCRIPTION/HYDROLASE / TRANSCRIPTION-HYDROLASE COMPLEX | |||||||||
Function / homology | ![]() response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / : / mating projection tip / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / : / mating projection tip / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATPase activator activity / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / P-body / 3'-5'-RNA exonuclease activity / molecular adaptor activity / negative regulation of translation / regulation of cell cycle / regulation of transcription by RNA polymerase II / RNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Basquin, J. / Conti, E. | |||||||||
![]() | ![]() Title: Architecture of the Nuclease Module of the Yeast Ccr4-not Complex: The not1-Caf1-Ccr4 Interaction. Authors: Basquin, J. / Roudko, V.V. / Rode, M. / Basquin, C. / Seraphin, B. / Conti, E. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 190.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 153.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 438.6 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b89C ![]() 4b8bC ![]() 4b8cC ![]() 1uocS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28527.402 Da / Num. of mol.: 1 / Fragment: MIF4G, RESIDUES 755-1000 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 33153.352 Da / Num. of mol.: 1 / Fragment: NUCLEASE DOMAIN, RESIDUES 151-433 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.51 % / Description: NONE |
---|---|
Crystal grow | pH: 8 Details: 8% (W/V) PEG 8000, 0.2 M NA MALONATE, 50 MM TRIS PH 8.0 AND 0.1% LOW MELTING AGAROSE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.7 Å / Num. obs: 27615 / % possible obs: 99.5 % / Observed criterion σ(I): 4.4 / Redundancy: 6 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.3→2.45 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 4.4 / % possible all: 96.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UOC Resolution: 2.4→60.14 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 23.24 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.622 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→60.14 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|