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Yorodumi- PDB-7daa: Crystal structure of basigin complexed with anti-basigin Fab fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 7daa | |||||||||||||||||||||
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Title | Crystal structure of basigin complexed with anti-basigin Fab fragment | |||||||||||||||||||||
Components |
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Keywords | CHAPERONE / Basigin / Fab / antibody / complex | |||||||||||||||||||||
Function / homology | Function and homology information Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / D-mannose binding / decidualization / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / Integrin cell surface interactions / response to cAMP / embryo implantation / neutrophil chemotaxis / Degradation of the extracellular matrix / photoreceptor inner segment / positive regulation of endothelial cell migration / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / virus receptor activity / melanosome / signaling receptor activity / basolateral plasma membrane / angiogenesis / endosome / cell surface receptor signaling pathway / positive regulation of viral entry into host cell / cadherin binding / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | |||||||||||||||||||||
Authors | Sakuragi, T. / Kanai, R. / Narita, H. / Onishi, E. / Miyazaki, T. / Baba, T. / Nakagawa, A. / Toyoshima, C. / Nagata, S. | |||||||||||||||||||||
Funding support | Japan, 6items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes. Authors: Takaharu Sakuragi / Ryuta Kanai / Akihisa Tsutsumi / Hirotaka Narita / Eriko Onishi / Kohei Nishino / Takuya Miyazaki / Takeshi Baba / Hidetaka Kosako / Atsushi Nakagawa / Masahide Kikkawa / ...Authors: Takaharu Sakuragi / Ryuta Kanai / Akihisa Tsutsumi / Hirotaka Narita / Eriko Onishi / Kohei Nishino / Takuya Miyazaki / Takeshi Baba / Hidetaka Kosako / Atsushi Nakagawa / Masahide Kikkawa / Chikashi Toyoshima / Shigekazu Nagata / Abstract: Xkr8-Basigin is a plasma membrane phospholipid scramblase activated by kinases or caspases. We combined cryo-EM and X-ray crystallography to investigate its structure at an overall resolution of 3. ...Xkr8-Basigin is a plasma membrane phospholipid scramblase activated by kinases or caspases. We combined cryo-EM and X-ray crystallography to investigate its structure at an overall resolution of 3.8 Å. Its membrane-spanning region carrying 22 charged amino acids adopts a cuboid-like structure stabilized by salt bridges between hydrophilic residues in transmembrane helices. Phosphatidylcholine binding was observed in a hydrophobic cleft on the surface exposed to the outer leaflet of the plasma membrane. Six charged residues placed from top to bottom inside the molecule were essential for scrambling phospholipids in inward and outward directions, apparently providing a pathway for their translocation. A tryptophan residue was present between the head group of phosphatidylcholine and the extracellular end of the path. Its mutation to alanine made the Xkr8-Basigin complex constitutively active, indicating that it plays a vital role in regulating its scramblase activity. The structure of Xkr8-Basigin provides insights into the molecular mechanisms underlying phospholipid scrambling. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7daa.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7daa.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 7daa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7daa_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 7daa_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 7daa_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 7daa_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7daa ftp://data.pdbj.org/pub/pdb/validation_reports/da/7daa | HTTPS FTP |
-Related structure data
Related structure data | 7d9zSC 7dceC S: Starting model for refinement 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: 19592.814 Da / Num. of mol.: 1 / Mutation: N152Q, N186Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BSG, UNQ6505/PRO21383 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35613 | ||
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#2: Antibody | Mass: 23319.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||
#3: Antibody | Mass: 22786.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||
#4: Chemical | ChemComp-CD / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.37 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris-HCl (pH 8.0) buffer containing 0.1M sodium chloride, 0.1M cadmium chloride hemi(pentahydrate), 33% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.509→123.676 Å / Num. obs: 18245 / % possible obs: 86.3 % / Redundancy: 5.1 % / CC1/2: 0.993 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.509→2.706 Å / Num. unique obs: 571 / CC1/2: 0.476 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7D9Z Resolution: 2.51→123.676 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→123.676 Å
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Refine LS restraints |
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LS refinement shell |
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