[English] 日本語
Yorodumi- PDB-8ujl: Crystal structure of human CTDNEP1-NEP1R1 protein phosphatase complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ujl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human CTDNEP1-NEP1R1 protein phosphatase complex | ||||||
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: 1.91 Å | ||||||
Authors | Gao, S. / Airola, M.V. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ujl.cif.gz | 176.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ujl.ent.gz | 117.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ujl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/8ujl ftp://data.pdbj.org/pub/pdb/validation_reports/uj/8ujl | HTTPS FTP |
---|
-Related structure data
Related structure data | 8ujmC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: CTDNEP1, CNEP1R1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95476, UniProt: H3BUT5 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→29.08 Å / SU ML: 0.2646 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4717 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -30.1150173489 Å / Origin y: -13.3384256528 Å / Origin z: -5.92299529952 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |