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- PDB-4h3h: Crystal structure of a ternary complex of human symplekin NTD, hu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h3h | ||||||
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Title | Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA poymerase II CTD peptide phosphorylated at SER-7 | ||||||
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![]() | HYDROLASE / Heat repeat / phosphatase / RNA polymerase II | ||||||
Function / homology | ![]() RNA polymerase II CTD heptapeptide repeat phosphatase activity / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / nuclear stress granule / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / myosin phosphatase activity / termination of RNA polymerase II transcription ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / nuclear stress granule / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / myosin phosphatase activity / termination of RNA polymerase II transcription / protein-serine/threonine phosphatase / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / bicellular tight junction / negative regulation of protein binding / mRNA processing / cytoskeleton / nuclear body / cell adhesion / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiang, K. / Tong, L. | ||||||
![]() | ![]() Title: An unexpected binding mode for a Pol II CTD peptide phosphorylated at Ser7 in the active site of the CTD phosphatase Ssu72. Authors: Xiang, K. / Manley, J.L. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 404.4 KB | Display | ![]() |
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PDB format | ![]() | 343 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39646.957 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 30-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 24758.787 Da / Num. of mol.: 2 / Mutation: C12S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NP77, protein-serine/threonine phosphatase #3: Protein/peptide | | Mass: 1099.042 Da / Num. of mol.: 1 / Source method: obtained synthetically #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.78 % |
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Crystal grow | Temperature: 293 K / pH: 8.5 Details: 1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate,, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2012 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 67207 / % possible obs: 99.9 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.2→2.32 Å / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.32 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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