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- PDB-8ujl: Crystal structure of human CTDNEP1-NEP1R1 protein phosphatase complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ujl | ||||||
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Title | Crystal structure of human CTDNEP1-NEP1R1 protein phosphatase complex | ||||||
![]() | CTD nuclear envelope phosphatase 1,Nuclear envelope phosphatase-regulatory subunit 1 | ||||||
![]() | HYDROLASE / phosphatase / nuclear envelope | ||||||
Function / homology | ![]() Nem1-Spo7 phosphatase complex / Depolymerization of the Nuclear Lamina / nuclear envelope organization / positive regulation of triglyceride biosynthetic process / mitotic nuclear membrane disassembly / gamete generation / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / mesoderm development ...Nem1-Spo7 phosphatase complex / Depolymerization of the Nuclear Lamina / nuclear envelope organization / positive regulation of triglyceride biosynthetic process / mitotic nuclear membrane disassembly / gamete generation / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / mesoderm development / protein localization to nucleus / canonical Wnt signaling pathway / positive regulation of protein dephosphorylation / lipid droplet / protein dephosphorylation / positive regulation of canonical Wnt signaling pathway / nuclear envelope / nuclear membrane / endoplasmic reticulum membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, S. / Airola, M.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and mechanism of the human CTDNEP1-NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology. Authors: Gao, S. / Carrasquillo Rodriguez, J.W. / Bahmanyar, S. / Airola, M.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.6 KB | Display | ![]() |
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PDB format | ![]() | 117.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.3 KB | Display | ![]() |
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Full document | ![]() | 436.9 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ujmC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31697.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fusion of human CTD nuclear envelope phosphatase 1 and human nuclear envelope phosphatase-regulatory subunit 1,Fusion of human CTD nuclear envelope phosphatase 1 and human nuclear envelope ...Details: Fusion of human CTD nuclear envelope phosphatase 1 and human nuclear envelope phosphatase-regulatory subunit 1,Fusion of human CTD nuclear envelope phosphatase 1 and human nuclear envelope phosphatase-regulatory subunit 1 Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 6% PEG 3350, 0.2 M lithium citrate, 0.4% CHAPS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2023 / Details: KB bimorph mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 1.908→29.08 Å / Num. obs: 23447 / % possible obs: 99.74 % / Redundancy: 2 % / Biso Wilson estimate: 32.92 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.05073 / Rpim(I) all: 0.05073 / Rrim(I) all: 0.07175 / Net I/σ(I): 7.92 |
Reflection shell | Resolution: 1.908→1.976 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7953 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 2260 / CC1/2: 0.412 / CC star: 0.764 / Rpim(I) all: 0.7953 / Rrim(I) all: 1.125 / % possible all: 98.01 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→29.08 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -30.1150173489 Å / Origin y: -13.3384256528 Å / Origin z: -5.92299529952 Å
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Refinement TLS group | Selection details: all |