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Yorodumi- PDB-8ujm: Crystal structure of human CTDNEP1-NEP1R1 protein phosphatase com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ujm | ||||||
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Title | Crystal structure of human CTDNEP1-NEP1R1 protein phosphatase complex with magnesium | ||||||
Components | CTD nuclear envelope phosphatase 1,Nuclear envelope phosphatase-regulatory subunit 1 | ||||||
Keywords | HYDROLASE / phosphatase / nuclear envelope | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.161 Å | ||||||
Authors | Gao, S. / Airola, M.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ujm.cif.gz | 238.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ujm.ent.gz | 156.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ujm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/8ujm ftp://data.pdbj.org/pub/pdb/validation_reports/uj/8ujm | HTTPS FTP |
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-Related structure data
Related structure data | 8ujlC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31697.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTDNEP1, CNEP1R1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95476, UniProt: H3BUT5 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.77 % |
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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: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 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: 2.161→50.45 Å / Num. obs: 30755 / % possible obs: 99.54 % / Redundancy: 2 % / Biso Wilson estimate: 33.65 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.09156 / Rpim(I) all: 0.09156 / Rrim(I) all: 0.1295 / Net I/σ(I): 5.67 |
Reflection shell | Resolution: 2.161→2.238 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7214 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3010 / CC1/2: 0.385 / CC star: 0.746 / Rpim(I) all: 0.7214 / Rrim(I) all: 1.02 / % possible all: 98.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.161→50.45 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3372 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: 47.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.161→50.45 Å
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Refine LS restraints |
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LS refinement shell |
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