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Open data
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Basic information
Entry | Database: PDB / ID: 4m6t | ||||||
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Title | Structure of human Paf1 and Leo1 complex | ||||||
![]() | RNA polymerase II-associated factor 1 homolog, Linker, RNA polymerase-associated protein LEO1 | ||||||
![]() | Transcription Regulator / Paf1-Leo1 subcomplex / transcription elongator | ||||||
Function / homology | ![]() RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / positive regulation of cell cycle G1/S phase transition / mRNA 3'-end processing / stem cell population maintenance / RNA polymerase II complex binding / protein localization to nucleus / RNA Polymerase II Transcription Elongation ...RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / positive regulation of cell cycle G1/S phase transition / mRNA 3'-end processing / stem cell population maintenance / RNA polymerase II complex binding / protein localization to nucleus / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / fibrillar center / Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to lipopolysaccharide / intracellular membrane-bounded organelle / centrosome / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shen, Y. / Qin, X. | ||||||
![]() | ![]() Title: Structural insights into Paf1 complex assembly and histone binding Authors: Chu, X. / Qin, X. / Xu, H. / Li, L. / Wang, Z. / Li, F. / Xie, X. / Zhou, H. / Shen, Y. / Long, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.9 KB | Display | ![]() |
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PDB format | ![]() | 34.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 702.3 KB | Display | ![]() |
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Full document | ![]() | 705.6 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21270.889 Da / Num. of mol.: 1 Fragment: UNP residues 170-250 of Paf1, UNP residues 370-462 of LEO1 Source method: isolated from a genetically manipulated source Details: chimera of RNA polymerase II-associated factor 1 homolog, Linker, RNA polymerase-associated protein LEO1 Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SAM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.72 Å3/Da / Density % sol: 73.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 3.5M sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.498→50 Å / Num. all: 14138 / Num. obs: 14136 / % possible obs: 99.75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 43.6 Å2 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.536 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.56 Å2 / Biso mean: 45.8081 Å2 / Biso min: 27.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.498→38.788 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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