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- EMDB-13155: Cryo-EM density of full-length rXKR9 in complex with a sybody at 3.66A -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13155 | |||||||||
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Title | Cryo-EM density of full-length rXKR9 in complex with a sybody at 3.66A | |||||||||
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Function / homology | XK-related protein / XK-related protein / phosphatidylserine exposure on apoptotic cell surface / engulfment of apoptotic cell / apoptotic process involved in development / membrane => GO:0016020 / membrane / plasma membrane / XK-related protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.66 Å | |||||||||
![]() | Straub MS / Sawicka M / Dutzler R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of the caspase-activated protein XKR9 involved in apoptotic lipid scrambling. Authors: Monique S Straub / Carolina Alvadia / Marta Sawicka / Raimund Dutzler / ![]() Abstract: The exposure of the negatively charged lipid phosphatidylserine on the cell surface, catalyzed by lipid scramblases, is an important signal for the clearance of apoptotic cells by macrophages. The ...The exposure of the negatively charged lipid phosphatidylserine on the cell surface, catalyzed by lipid scramblases, is an important signal for the clearance of apoptotic cells by macrophages. The protein XKR9 is a member of a conserved family that has been associated with apoptotic lipid scrambling. Here, we describe structures of full-length and caspase-treated XKR9 from in complex with a synthetic nanobody determined by cryo-electron microscopy. The 43 kDa monomeric membrane protein can be divided into two structurally related repeats, each containing four membrane-spanning segments and a helix that is partly inserted into the lipid bilayer. In the full-length protein, the C-terminus interacts with a hydrophobic pocket located at the intracellular side acting as an inhibitor of protein function. Cleavage by caspase-3 at a specific site releases 16 residues of the C-terminus, thus making the pocket accessible to the cytoplasm. Collectively, the work has revealed the unknown architecture of the XKR family and has provided initial insight into its activation by caspases. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 21 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.3 KB | Display | ![]() |
Images | ![]() | 383.7 KB | ||
Masks | ![]() | 22.2 MB | ![]() | |
Others | ![]() ![]() | 20.6 MB 20.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 341.4 KB | Display | ![]() |
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Full document | ![]() | 340.5 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p14MC ![]() 7p16C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.302 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13155_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13155_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : rXKR9 with sybody
Entire | Name: rXKR9 with sybody |
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Components |
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-Supramolecule #1: rXKR9 with sybody
Supramolecule | Name: rXKR9 with sybody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 17 KDa |
-Supramolecule #2: rXKR9
Supramolecule | Name: rXKR9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: Sybody
Supramolecule | Name: Sybody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: XK-related protein
Macromolecule | Name: XK-related protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.563059 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MKYTICNFMM SVLGIIIYVT DLVADIVLTV RYFYDGQYVF GVLTLSFVLC GTLIVHCFSY SWLKDDLKKA GGENEHYFLL LHCLQGGVF TRYWFVLRTG YHVVFKHSHR TSNFMEEQTD PHKEAIDMAT DLSMLRLFET YLEGCPQLIL QLYAFLERGQ A NFSQYMVI ...String: MKYTICNFMM SVLGIIIYVT DLVADIVLTV RYFYDGQYVF GVLTLSFVLC GTLIVHCFSY SWLKDDLKKA GGENEHYFLL LHCLQGGVF TRYWFVLRTG YHVVFKHSHR TSNFMEEQTD PHKEAIDMAT DLSMLRLFET YLEGCPQLIL QLYAFLERGQ A NFSQYMVI MVSCCAISWS TVDYQIALRK SLPDKNLLRG FWPKLTYLFY KLFTLLSWML SVVLLLFVDV RTVLLLLLFL WT VGFIWAF INHTQFCNSL SMEFLYRLVV GFILVFTFFN IKGQNTKCPM SCYYTVRVLG TLGILTVFWI YPLSIFNSDY FIP ISATIV LSLLFGIIFL GVYYGTYHPN INAGTQHDEP DGKAPQRDCR IRYFLMDA |
-Macromolecule #2: Sybody
Macromolecule | Name: Sybody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 13.675293 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SQVQLVESGG GSVQAGGSLR LSCAASGNIA DIYYLGWFRQ APGKEREGVA ALITYNGRTY YADSVKGRFT VSLDNAKNTV YLQMNSLKP EDTALYYCAA AYNGLIAAPL KVTRYWYWGQ GTQVTVS |
-Macromolecule #3: DIUNDECYL PHOSPHATIDYL CHOLINE
Macromolecule | Name: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PLC |
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Molecular weight | Theoretical: 622.834 Da |
Chemical component information | ![]() ChemComp-PLC: |
-Macromolecule #4: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...
Macromolecule | Name: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine type: ligand / ID: 4 / Number of copies: 1 / Formula: P5S |
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Molecular weight | Theoretical: 792.075 Da |
Chemical component information | ![]() ChemComp-P5S: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | This sample was monodisperse |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 12396 / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7p14: |