+
Open data
-
Basic information
Entry | Database: PDB / ID: 7smd | ||||||
---|---|---|---|---|---|---|---|
Title | p107 pocket domain complexed with EID1 peptide | ||||||
![]() |
| ||||||
![]() | CELL CYCLE / Transcription / cyclin box pocket transcriptional regulator | ||||||
Function / homology | ![]() histone acetyltransferase regulator activity / regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / histone acetyltransferase binding / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / regulation of cell differentiation / negative regulation of cellular senescence / G0 and Early G1 ...histone acetyltransferase regulator activity / regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / histone acetyltransferase binding / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / regulation of cell differentiation / negative regulation of cellular senescence / G0 and Early G1 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cytoplasmic ribonucleoprotein granule / transcription corepressor activity / Cyclin D associated events in G1 / chromatin organization / transcription regulator complex / cell differentiation / cell cycle / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Putta, S. / Fernandez, S.M. / Tripathi, S.M. / Muller, G.A. / Rubin, S.M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family. Authors: Putta, S. / Alvarez, L. / Ludtke, S. / Sehr, P. / Muller, G.A. / Fernandez, S.M. / Tripathi, S. / Lewis, J. / Gibson, T.J. / Chemes, L.B. / Rubin, S.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 88.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 456.9 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7smcC ![]() 7smeC ![]() 7smfC ![]() 4yosS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 43265.965 Da / Num. of mol.: 1 / Fragment: UNP residues 391-601,780-887,924-972 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 1635.769 Da / Num. of mol.: 1 / Fragment: UNP residues 174-187 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→33.92 Å / Num. obs: 27480 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.15→2.22 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2385 / CC1/2: 0.69 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 4YOS Resolution: 2.15→33.92 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.47 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→33.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|