8XEJ

Cryo-EM structure of human XKR8-basigin complex in lipid nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The role of the C-terminal tail region as a plug to regulate XKR8 lipid scramblase.

Sakuragi, T.Kanai, R.Otani, M.Kikkawa, M.Toyoshima, C.Nagata, S.

(2024) J Biol Chem 300: 105755-105755

  • DOI: https://doi.org/10.1016/j.jbc.2024.105755
  • Primary Citation of Related Structures:  
    8XEJ

  • PubMed Abstract: 

    XKR8, in complex with the transmembrane glycoprotein basigin, functions as a phospholipid scramblase activated by the caspase-mediated cleavage or phosphorylation of its C-terminal tail. It carries a putative phospholipid translocation path of multiple hydrophobic and charged residues in the transmembrane region. It also has a crucial tryptophan at the exoplasmic end of the path that regulates its scrambling activity. We herein investigated the tertiary structure of the human XKR8/basigin complex embedded in lipid nanodiscs at an overall resolution of 3.66 Å. We found that the C-terminal tail engaged in intricate polar and van der Waals interactions with a groove at the cytoplasmic surface of XKR8. These interactions maintained the inactive state of XKR8. Point mutations to disrupt these interactions strongly enhanced the scrambling activity of XKR8, suggesting that the activation of XKR8 is mediated by releasing the C-terminal tail from the cytoplasmic groove. We speculate that the cytoplasmic tail region of XKR8 functions as a plug to prevent the scrambling of phospholipids.


  • Organizational Affiliation

    Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Osaka, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of BasiginA [auth B]176Homo sapiensMutation(s): 2 
Gene Names: BSG
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P35613 (Homo sapiens)
Explore P35613 
Go to UniProtKB:  P35613
PHAROS:  P35613
GTEx:  ENSG00000172270 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35613
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
XK-related protein 8B [auth X]405Homo sapiensMutation(s): 0 
Gene Names: XKR8XRG8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6D3 (Homo sapiens)
Explore Q9H6D3 
Go to UniProtKB:  Q9H6D3
GTEx:  ENSG00000158156 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H6D3
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainC [auth H]217Oryctolagus cuniculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainD [auth L]218Oryctolagus cuniculusMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DLP (Subject of Investigation/LOI)
Query on DLP

Download Ideal Coordinates CCD File 
E [auth X]1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H80 N O8 P
FVXDQWZBHIXIEJ-LNDKUQBDSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
C [auth H]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan22K06102
Japan Society for the Promotion of Science (JSPS)JapanA21H04770
Japan Agency for Medical Research and Development (AMED)JapanJP23ama121002

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references