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- EMDB-30636: Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment -

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Basic information

Entry
Database: EMDB / ID: EMD-30636
TitleCryo-EM structure of human XKR8-basigin complex bound to Fab fragment
Map dataCryo-EM map for human XKR8/Basigin complex bound to Fab fragment
Sample
  • Complex: human XKR8-basigin complex bound to Fab fragment
    • 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: Heavy chain of Fab fragment
      • Protein or peptide: Light chain of Fab fragment
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsXKR8 / basigin / scramblase / phospholipid / TRANSPORT PROTEIN
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 / tolerance induction to self antigen / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / phospholipid scramblase activity / neutrophil clearance / response to mercury ion / engulfment of apoptotic cell ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / phosphatidylserine exposure on apoptotic cell surface / tolerance induction to self antigen / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / phospholipid scramblase activity / neutrophil clearance / response to mercury ion / engulfment of apoptotic cell / endothelial tube morphogenesis / neural retina development / apoptotic process involved in development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / D-mannose binding / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / positive regulation of myoblast differentiation / Integrin cell surface interactions / response to cAMP / Degradation of the extracellular matrix / photoreceptor inner segment / embryo implantation / neutrophil chemotaxis / positive regulation of endothelial cell migration / protein localization to plasma membrane / establishment of localization in cell / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / signaling receptor activity / virus receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / intracellular membrane-bounded organelle / 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: 3.8 Å
AuthorsSakuragi T / Kanai R
Funding support Japan, 7 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H05785 Japan
Japan Society for the Promotion of Science (JSPS)20K15731 Japan
Japan Science and TechnologyJPMJCR14M1 Japan
Japan Science and TechnologyJPMJCR14M4 Japan
Japan Agency for Medical Research and Development (AMED)JP17am010172 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101072 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101072 Japan
CitationJournal: 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
DepositionOct 26, 2020-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0552
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0552
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dce
  • Surface level: 0.0552
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30636.png

Downloads & links

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Map

FileDownload / File: emd_30636.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map for human XKR8/Basigin complex bound to Fab fragment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 160 pix.
= 199.2 Å		1.25 Å/pix.
x 160 pix.
= 199.2 Å		1.25 Å/pix.
x 160 pix.
= 199.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0552 / Movie #1: 0.0552
Minimum - Maximum-0.25718895 - 0.4062504
Average (Standard dev.)0.00086290436 (±0.010654351)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 199.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2451.2451.245
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z199.200199.200199.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-250-250-250
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.2570.4060.001

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Supplemental data

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Sample components

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Entire : human XKR8-basigin complex bound to Fab fragment

EntireName: human XKR8-basigin complex bound to Fab fragment
Components
  • Complex: human XKR8-basigin complex bound to Fab fragment
    • 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: Heavy chain of Fab fragment
      • Protein or peptide: Light chain of Fab fragment
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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

SupramoleculeName: human XKR8-basigin complex bound to Fab fragment / 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: Heavy chain of Fab fragment

MacromoleculeName: Heavy chain of Fab fragment / 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: Light chain of Fab fragment

MacromoleculeName: Light chain of Fab fragment / 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: 48.0 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: 0.8 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62124
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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