[English] 日本語
![](img/lk-miru.gif)
- PDB-8a8f: Crystal structure of Glc7 phosphatase in complex with the regulat... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8a8f | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Glc7 phosphatase in complex with the regulatory region of Ref2 | |||||||||
![]() |
| |||||||||
![]() | GENE REGULATION / Ser/Thr phosphatase / regulatory subunit / RNA / transcription termination | |||||||||
Function / homology | ![]() regulation of cell budding / regulation of protein localization to cell division site involved in cytokinesis / mating projection base / cellular bud neck septin collar / : / positive regulation of mitotic actomyosin contractile ring assembly / regulation of cellular response to glucose starvation / : / negative regulation of protein serine/threonine phosphatase activity / sno(s)RNA 3'-end processing ...regulation of cell budding / regulation of protein localization to cell division site involved in cytokinesis / mating projection base / cellular bud neck septin collar / : / positive regulation of mitotic actomyosin contractile ring assembly / regulation of cellular response to glucose starvation / : / negative regulation of protein serine/threonine phosphatase activity / sno(s)RNA 3'-end processing / positive regulation of clathrin-dependent endocytosis / termination of RNA polymerase II transcription, poly(A)-coupled / protein phosphatase type 1 complex / ascospore formation / cellular bud site selection / regulation of glycogen biosynthetic process / regulation of glycogen metabolic process / incipient cellular bud site / intracellular monoatomic ion homeostasis / mRNA cleavage and polyadenylation specificity factor complex / negative regulation of actin filament polymerization / DNA replication checkpoint signaling / cellular bud neck / mRNA 3'-end processing / spindle pole body / protein localization to kinetochore / : / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / mitotic spindle assembly checkpoint signaling / replication fork processing / cell division site / response to unfolded protein / chromosome organization / regulation of mitotic cell cycle / telomere maintenance / meiotic cell cycle / DNA damage checkpoint signaling / chromosome segregation / kinetochore / regulation of cell shape / response to heat / regulation of cell cycle / chromatin binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Carminati, M. / Manav, C.M. / Bellini, D. / Passmore, L.A. | |||||||||
Funding support | European Union, 2items
| |||||||||
![]() | ![]() Title: A direct interaction between CPF and RNA Pol II links RNA 3' end processing to transcription. Authors: Manuel Carminati / Juan B Rodríguez-Molina / M Cemre Manav / Dom Bellini / Lori A Passmore / ![]() Abstract: Transcription termination by RNA polymerase II (RNA Pol II) is linked to RNA 3' end processing by the cleavage and polyadenylation factor (CPF or CPSF). CPF contains endonuclease, poly(A) polymerase, ...Transcription termination by RNA polymerase II (RNA Pol II) is linked to RNA 3' end processing by the cleavage and polyadenylation factor (CPF or CPSF). CPF contains endonuclease, poly(A) polymerase, and protein phosphatase activities, which cleave and polyadenylate pre-mRNAs and dephosphorylate RNA Pol II to control transcription. Exactly how the RNA 3' end processing machinery is coupled to transcription remains unclear. Here, we combine in vitro reconstitution, structural studies, and genome-wide analyses to show that yeast CPF physically and functionally interacts with RNA Pol II. Surprisingly, CPF-mediated dephosphorylation promotes the formation of an RNA Pol II stalk-to-stalk homodimer in vitro. This dimer is compatible with transcription but not with the binding of transcription elongation factors. Disruption of the dimerization interface in cells causes transcription defects, including altered RNA Pol II abundance on protein-coding genes, tRNA genes, and intergenic regions. We hypothesize that RNA Pol II dimerization may provide a mechanistic basis for the allosteric model of transcription termination. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 90.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 66.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 460.5 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qwjS 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: 36036.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The Glc7 C-terminus is covalently linked to chain B (Ref2 348-405) Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GLC7, CID1, DIS2, YER133W / Plasmid: pET24a Production host: ![]() ![]() References: UniProt: P32598, protein-serine/threonine phosphatase | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 8500.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: To trap the Glc7 substrate in the active site, two RNA Pol II CTD repeats were fused C-terminally of Ref2 348-405. The substrate was not visible in the crystal structure. Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: REF2, YDR195W, YD9346.06 Production host: ![]() ![]() References: UniProt: P42073 | ||||||
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 40 % (v/v) 1,4-Butanediol and 0.1 M Tris-HCl pH 8.5 PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→45.12 Å / Num. obs: 41059 / % possible obs: 99.96 % / Redundancy: 10 % / CC1/2: 1 / Rmerge(I) obs: 0.04671 / Net I/σ(I): 20.46 |
Reflection shell | Resolution: 1.85→1.917 Å / Redundancy: 10 % / Rmerge(I) obs: 1.224 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 4028 / CC1/2: 0.9 / % possible all: 98.82 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7QWJ Resolution: 1.85→45.12 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.08 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.67 Å2 / Biso mean: 54.6302 Å2 / Biso min: 33.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→45.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
|