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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 data
Samplehuman XKR8-basigin complex bound to Fab fragment:
human XKR8-basigin complex / Fab fragmentFragment antigen-binding / Isoform 2 of Basigin / XK-related protein 8 / Heavy chain of Fab fragment / Light chain of Fab fragment / ligand
Function / homology
Function and homology information


phosphatidylserine exposure on apoptotic cell surface / Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / tolerance induction to self antigen / Proton-coupled monocarboxylate transport / establishment of localization in cell / acrosomal membrane / positive regulation of matrix metallopeptidase secretion / dendrite self-avoidance / cell-cell adhesion mediator activity / neural retina development ...phosphatidylserine exposure on apoptotic cell surface / Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / tolerance induction to self antigen / Proton-coupled monocarboxylate transport / establishment of localization in cell / acrosomal membrane / positive regulation of matrix metallopeptidase secretion / dendrite self-avoidance / cell-cell adhesion mediator activity / neural retina development / response to mercury ion / endothelial tube morphogenesis / engulfment of apoptotic cell / Pyruvate metabolism / apoptotic process involved in development / photoreceptor cell maintenance / Basigin interactions / positive regulation of viral entry into host cell / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / homophilic cell adhesion via plasma membrane adhesion molecules / mannose binding / decidualization / embryo implantation / Integrin cell surface interactions / response to cAMP / response to peptide hormone / Degradation of the extracellular matrix / neutrophil chemotaxis / protein localization to plasma membrane / positive regulation of endothelial cell migration / photoreceptor inner segment / sarcolemma / positive regulation of interleukin-6 production / odontogenesis of dentin-containing tooth / axon guidance / melanosome / virus receptor activity / signaling receptor activity / angiogenesis / basolateral plasma membrane / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / axon / membrane raft / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / integral component of plasma membrane / mitochondrion / extracellular exosome / membrane / integral component of membrane / plasma membrane
Similarity search - Function
XK-related protein / XK-related protein / Basigin / Basigin-like / Immunoglobulin C-2 Type / Immunoglobulin subtype 2 / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...XK-related protein / XK-related protein / Basigin / Basigin-like / Immunoglobulin C-2 Type / Immunoglobulin subtype 2 / 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 / Tsutsumi A / Narita H / Onishi E / Miyazaki T / Baba T / Nakagawa A / Kikkawa M / Toyoshima C / Nagata S
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-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing 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
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  • 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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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)
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
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 / Number of Components: 8

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Component #1: protein, human XKR8-basigin complex bound to Fab fragment

ProteinName: human XKR8-basigin complex bound to Fab fragment / Recombinant expression: No
MassTheoretical: 110 kDa

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Component #2: protein, human XKR8-basigin complex

ProteinName: human XKR8-basigin complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, Fab fragment

ProteinName: Fab fragmentFragment antigen-binding / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Isoform 2 of Basigin

ProteinName: Isoform 2 of Basigin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.592814 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #5: protein, XK-related protein 8

ProteinName: XK-related protein 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.975609 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #6: protein, Heavy chain of Fab fragment

ProteinName: Heavy chain of Fab fragment / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.869639 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Light chain of Fab fragment

ProteinName: Light chain of Fab fragment / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.261865 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: ligand, 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

LigandName: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.782082 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 48 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 62124
3D reconstructionResolution: 3.8 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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