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Yorodumi- PDB-6j0o: Crystal structure of CERT START domain in complex with compound SC1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j0o | ||||||
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Title | Crystal structure of CERT START domain in complex with compound SC1 | ||||||
Components | LIPID-TRANSFER PROTEIN CERT | ||||||
Keywords | LIPID TRANSPORT / CERT / PH / START / COMPLEX | ||||||
Function / homology | Function and homology information intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / ceramide binding / ceramide metabolic process / intermembrane lipid transfer / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / ceramide binding / ceramide metabolic process / intermembrane lipid transfer / Sphingolipid de novo biosynthesis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / lipid homeostasis / heart morphogenesis / response to endoplasmic reticulum stress / mitochondrion organization / muscle contraction / cell morphogenesis / kinase activity / in utero embryonic development / cell population proliferation / immune response / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Suzuki, M. / Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Kobayashi, S. / Hanada, K. | ||||||
Citation | Journal: Commun Chem / Year: 2019 Title: Natural ligand-nonmimetic inhibitors of the lipid-transfer protein CERT Authors: Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Suzuki, M. / Kobayashi, S. / Hanada, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j0o.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j0o.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 6j0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j0o ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j0o | HTTPS FTP |
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-Related structure data
Related structure data | 5zygC 5zyhC 5zyiC 5zyjC 5zykC 5zylC 5zymC 6iezC 6if0C 6j81C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27056.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CERT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5P4 |
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#2: Chemical | ChemComp-XAF / |
#3: Chemical | ChemComp-UNX / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | UNX 601 was modeled on an electron density peak clearly observed near methylpyridine moiety of XAF. ...UNX 601 was modeled on an electron density peak clearly observed near methylpyridine moiety of XAF. However distances between this peak and surrounding H-bond donor/acceptor are too short. Therefore it is assigned to unknown atom, not to water oxygen. |
Sequence details | Authors state that these amino residues are originated from protease site after N-terminal affinity tag. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.1M trisodium citrate/HCL buffer, pH5.9 containing 24% PEG3350 and 0.2% n-octyl-beta-D-glucoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 10, 2014 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30.13 Å / Num. obs: 27078 / % possible obs: 99.8 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Net I/σ(I): 16.4 / Num. measured all: 122989 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.617 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.37 Å2 / Biso mean: 26.48 Å2 / Biso min: 13.38 Å2
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Refinement step | Cycle: final / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.863 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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