[English] 日本語
![](img/lk-miru.gif)
- PDB-4a64: Crystal structure of the N-terminal domain of human Cul4B at 2.57... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4a64 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal domain of human Cul4B at 2.57A resolution | ||||||
![]() | CULLIN-4B | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() Cul4-RING E3 ubiquitin ligase complex / astrocyte differentiation / UV-damage excision repair / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of G1/S transition of mitotic cell cycle / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / G1/S transition of mitotic cell cycle ...Cul4-RING E3 ubiquitin ligase complex / astrocyte differentiation / UV-damage excision repair / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of G1/S transition of mitotic cell cycle / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / G1/S transition of mitotic cell cycle / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / cellular response to UV / neuron projection development / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vollmar, M. / Ayinampudi, V. / Cooper, C. / Guo, K. / Krojer, T. / Muniz, J.R.C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. ...Vollmar, M. / Ayinampudi, V. / Cooper, C. / Guo, K. / Krojer, T. / Muniz, J.R.C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Bullock, A. | ||||||
![]() | ![]() Title: Crystal Structure of the N-Terminal Domain of Human Cul4B at 2.57A Resolution Authors: Vollmar, M. / Ayinampudi, V. / Cooper, C. / Guo, K. / Krojer, T. / Muniz, J.R.C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Bullock, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 563.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 470.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 41952.062 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 188-539 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / ![]() #3: Water | ChemComp-HOH / | ![]() Compound details | ENGINEERED RESIDUE IN CHAIN A, VAL 498 TO ARG ENGINEERED RESIDUE IN CHAIN A, LEU 502 TO ASP ...ENGINEERED | Sequence details | STARTING RESIDUES SER186 AND MET187 ARE DUE TO CLONING | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.92 % / Description: NONE |
---|---|
Crystal grow![]() | Details: 24% PEG4000, 100 MM LISO4, 100 MM TRIS (PH 8.2) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.57→19.97 Å / Num. obs: 58043 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.57→2.71 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE Resolution: 2.57→19.74 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 20.02 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.529 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 51.113 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57→19.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|