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- EMDB-38291: Cryo-EM structure of human XKR8-basigin complex in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-38291
TitleCryo-EM structure of human XKR8-basigin complex in lipid nanodisc
Map data
Sample
  • Complex: human XKR8-basigin complex bound to Fab fragment in lipid nanodisc
    • Complex: human XKR8-basigin complex
      • Protein or peptide: Isoform 2 of Basigin
      • Protein or peptide: XK-related protein 8
    • Complex: Fab fragment
      • Protein or peptide: Fab heavy chain
      • Protein or peptide: Fab light chain
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Keywordsscramblase / apoptosis / membrane protein / LIPID TRANSPORT
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / phosphatidylserine exposure on apoptotic cell surface / positive regulation of matrix metallopeptidase secretion / tolerance induction to self antigen / dendrite self-avoidance / acrosomal membrane / neutrophil clearance / phospholipid scramblase activity / cell-cell adhesion mediator activity ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / phosphatidylserine exposure on apoptotic cell surface / positive regulation of matrix metallopeptidase secretion / tolerance induction to self antigen / dendrite self-avoidance / acrosomal membrane / neutrophil clearance / phospholipid scramblase activity / cell-cell adhesion mediator activity / endothelial tube morphogenesis / response to mercury ion / engulfment of apoptotic cell / neural retina development / apoptotic process involved in development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / D-mannose binding / homophilic cell-cell adhesion / odontogenesis of dentin-containing tooth / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / response to cAMP / Integrin cell surface interactions / positive regulation of myoblast differentiation / Degradation of the extracellular matrix / neutrophil chemotaxis / photoreceptor inner segment / embryo implantation / positive regulation of endothelial cell migration / axon guidance / protein localization to plasma membrane / establishment of localization in cell / response to peptide hormone / sarcolemma / positive regulation of interleukin-6 production / melanosome / signaling receptor activity / virus receptor activity / angiogenesis / basolateral plasma membrane / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / axon / focal adhesion / endoplasmic reticulum membrane / perinuclear region of cytoplasm / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
XK-related protein / : / XK-related protein / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...XK-related protein / : / XK-related protein / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Basigin / XK-related protein 8
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsSakuragi TS / Kanai RK / Kikkawa MK / Toyoshima CT / Nagata SN
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K06102 Japan
Japan Society for the Promotion of Science (JSPS)A21H04770 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121002 Japan
CitationJournal: J Biol Chem / Year: 2024
Title: The role of the C-terminal tail region as a plug to regulate XKR8 lipid scramblase.
Authors: Takaharu Sakuragi / Ryuta Kanai / Mayumi Otani / Masahide Kikkawa / Chikashi Toyoshima / Shigekazu Nagata /
Abstract: XK-related 8 (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 ...XK-related 8 (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.
History
DepositionDec 12, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38291.png

Downloads & links

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Map

FileDownload / File: emd_38291.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 256 pix.
= 315.4 Å		1.23 Å/pix.
x 256 pix.
= 315.4 Å		1.23 Å/pix.
x 256 pix.
= 315.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23203 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.208
Minimum - Maximum-1.2436364 - 1.908299
Average (Standard dev.)0.00062022195 (±0.026462037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 315.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38291_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38291_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : human XKR8-basigin complex bound to Fab fragment in lipid nanodisc

EntireName: human XKR8-basigin complex bound to Fab fragment in lipid nanodisc
Components
  • Complex: human XKR8-basigin complex bound to Fab fragment in lipid nanodisc
    • Complex: human XKR8-basigin complex
      • Protein or peptide: Isoform 2 of Basigin
      • Protein or peptide: XK-related protein 8
    • Complex: Fab fragment
      • Protein or peptide: Fab heavy chain
      • Protein or peptide: Fab light chain
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: human XKR8-basigin complex bound to Fab fragment in lipid nanodisc

SupramoleculeName: human XKR8-basigin complex bound to Fab fragment in lipid nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 110 KDa

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Supramolecule #2: human XKR8-basigin complex

SupramoleculeName: human XKR8-basigin complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Fab fragment

SupramoleculeName: Fab fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Isoform 2 of Basigin

MacromoleculeName: Isoform 2 of Basigin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.592814 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
AGPPRVKAVK SSEHINEGET AMLVCKSESV PPVTDWAWYK ITDSEDKALM QGSESRFFVS SSQGRSELHI ENLNMEADPG QYRCQGTSS KGSDQAIITL RVRSHLAALW PFLGIVAEVL VLVTIIFIYE KRRKPEDVLD DDDAGSAPLK SSGQHQNDKG K NVRQRNSS DYKDDDDK

UniProtKB: Basigin

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Macromolecule #2: XK-related protein 8

MacromoleculeName: XK-related protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.975609 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPWSSRGALL RDLVLGVLGT AAFLLDLGTD LWAAVQYALG GRYLWAALVL ALLGLASVAL QLFSWLWLRA DPAGLHGSQP PRRCLALLH LLQLGYLYRC VQELRQGLLV WQQEEPSEFD LAYADFLALD ISMLRLFETF LETAPQLTLV LAIMLQSGRA E YYQWVGIC ...String:
MPWSSRGALL RDLVLGVLGT AAFLLDLGTD LWAAVQYALG GRYLWAALVL ALLGLASVAL QLFSWLWLRA DPAGLHGSQP PRRCLALLH LLQLGYLYRC VQELRQGLLV WQQEEPSEFD LAYADFLALD ISMLRLFETF LETAPQLTLV LAIMLQSGRA E YYQWVGIC TSFLGISWAL LDYHRALRTC LPSKPLLGLG SSVIYFLWNL LLLWPRVLAV ALFSALFPSY VALHFLGLWL VL LLWVWLQ GTDFMPDPSS EWLYRVTVAT ILYFSWFNVA EGRTRGRAII HFAFLLSDSI LLVATWVTHS SWLPSGIPLQ LWL PVGCGC FFLGLALRLV YYHWLHPSCC WKPDPDQVDG ARSLLSPEGY QLPQNRRMTH LAQKFFPKAK DEAASPVKGV DEFE NLYFQ

UniProtKB: XK-related protein 8

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Macromolecule #3: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 22.869639 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (PCA)SVEESGGRL VTPGTPLTLT CTVSGFSLSD YAMNWVRQAP GKGLEWIGII YASGSRYYAS WAKGRFTISK TSTTVD LKI TSPTTEDTAT YFCARYYAGS DIWGPGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV TVSWNSG AL TSGVHTFPAV ...String:
(PCA)SVEESGGRL VTPGTPLTLT CTVSGFSLSD YAMNWVRQAP GKGLEWIGII YASGSRYYAS WAKGRFTISK TSTTVD LKI TSPTTEDTAT YFCARYYAGS DIWGPGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV TVSWNSG AL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDK

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Macromolecule #4: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 23.261865 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ADVVMTQTPS SVSAAVGGTV TINCQASQSI SAYLAWYQQK PGQPPKLLIY DASDLASGVS SRFKGSGSGT QFTLTISALE CADAATYYC QSYYAIITYG AAFGGGTEVV VKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT ...String:
ADVVMTQTPS SVSAAVGGTV TINCQASQSI SAYLAWYQQK PGQPPKLLIY DASDLASGVS SRFKGSGSGT QFTLTISALE CADAATYYC QSYYAIITYG AAFGGGTEVV VKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT EQDSKDCTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

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Macromolecule #5: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: DLP
Molecular weightTheoretical: 782.082 Da
Chemical component information

ChemComp-DLP:
1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162528
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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