- PDB-7p14: Structure of full-length rXKR9 in complex with a sybody at 3.66A -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7p14
Title
Structure of full-length rXKR9 in complex with a sybody at 3.66A
Components
Sybody
XK-related protein
Keywords
MEMBRANE PROTEIN / small membrane protein / in complex with sybody / apoptotic lipid scrambling
Function / homology
Function and homology information
phosphatidylserine exposure on apoptotic cell surface / engulfment of apoptotic cell / apoptotic process involved in development / membrane => GO:0016020 / membrane / plasma membrane Similarity search - Function
Journal: Elife / Year: 2021 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.
Mass: 792.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO10P
Has ligand of interest
N
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Experimental details
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Experiment
Experiment
Method: ELECTRON MICROSCOPY
EM experiment
Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
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Sample preparation
Component
ID
Name
Type
Entity ID
Parent-ID
Source
1
rXKR9withsybody
COMPLEX
#1-#2
0
RECOMBINANT
2
rXKR9
COMPLEX
#1
1
RECOMBINANT
3
Sybody
COMPLEX
#2
1
RECOMBINANT
Molecular weight
ID
Entity assembly-ID
Value (°)
Experimental value
1
1
0.06MDa
NO
2
1
0.043MDa
NO
3
1
0.017MDa
NO
Source (natural)
ID
Entity assembly-ID
Organism
Ncbi tax-ID
2
1
Rattus norvegicus (Norway rat)
10116
3
2
Rattus norvegicus (Norway rat)
10116
4
3
synthetic construct (others)
32630
Source (recombinant)
ID
Entity assembly-ID
Organism
Ncbi tax-ID
2
1
Homo sapiens (human)
9606
3
2
Homo sapiens (human)
9606
4
3
Escherichia coli MC1061 (bacteria)
1211845
Buffer solution
pH: 7.5
Buffer component
ID
Conc.
Name
Formula
Buffer-ID
1
200mM
sodiumchloride
NaCl
1
2
25mM
HEPES
HEPES
1
3
0.01 %
LaurylMaltoseNeopentylGlycol
LMNG
1
Specimen
Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
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