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- EMDB-44744: Structure of human Xk-related protein 4 -

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Basic information

Entry
Database: EMDB / ID: EMD-44744
TitleStructure of human Xk-related protein 4
Map dataStructure of human Xk-related protein 4
Sample
  • Complex: Monomeric human Xkr-related protein 4
    • Protein or peptide: XK-related protein 4
KeywordsPhospholipid scramblase / apoptosis / MEMBRANE PROTEIN
Function / homologyXK-related protein / : / XK-related protein / phosphatidylserine exposure on apoptotic cell surface / engulfment of apoptotic cell / apoptotic process involved in development / plasma membrane / XK-related protein 4
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChakraborty S / Accardi A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structure and function of the human apoptotic scramblase Xkr4.
Authors: Sayan Chakraborty / Zhang Feng / Sangyun Lee / Omar E Alvarenga / Aniruddha Panda / Shuming Zhang / Renato Bruni / George Khelashvili / Kallol Gupta / Alessio Accardi /
Abstract: Phosphatidylserine externalization on the surface of dying cells is a key signal for their recognition and clearance by macrophages and is mediated by members of the X-Kell related (Xkr) protein ...Phosphatidylserine externalization on the surface of dying cells is a key signal for their recognition and clearance by macrophages and is mediated by members of the X-Kell related (Xkr) protein family. Defective Xkr-mediated scrambling impairs clearance, leading to inflammation. It was proposed that activation of the Xkr4 apoptotic scramblase requires caspase cleavage, followed by dimerization and ligand binding. Here, using a combination of biochemical approaches we show that purified monomeric, full-length human Xkr4 (hXkr4) scrambles lipids. CryoEM imaging shows that hXkr4 adopts a novel conformation, where three conserved acidic residues create a negative electrostatic surface embedded in the membrane. Molecular dynamics simulations show this conformation induces membrane thinning, which could promote scrambling. Thinning is ablated or reduced in conditions where scrambling is abolished or reduced. Our work provides insights into the molecular mechanisms of hXkr4 scrambling and suggests the ability to thin membranes might be a general property of active scramblases.
History
DepositionMay 3, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44744.png

Downloads & links

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Map

FileDownload / File: emd_44744.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of human Xk-related protein 4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.37
Minimum - Maximum-1.4006556 - 2.3161323
Average (Standard dev.)0.0008171152 (±0.041100528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_44744_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_44744_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Monomeric human Xkr-related protein 4

EntireName: Monomeric human Xkr-related protein 4
Components
  • Complex: Monomeric human Xkr-related protein 4
    • Protein or peptide: XK-related protein 4

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Supramolecule #1: Monomeric human Xkr-related protein 4

SupramoleculeName: Monomeric human Xkr-related protein 4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.5 kDa/nm

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Macromolecule #1: XK-related protein 4

MacromoleculeName: XK-related protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.569625 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MAAKSDGRLK MKKSSDVAFT PLQNSDHSGS VQGLAPGLPS GSGAEDEEAA GGGCCPDGGG CSRCCCCCAG SGGSAGSGGS GGVAGPGGG GAGSAALCLR LGREQRRYSL WDCLWILAAV AVYFADVGTD VWLAVDYYLR GQRWWFGLTL FFVVLGSLSV Q VFSFRWFV ...String:
MAAKSDGRLK MKKSSDVAFT PLQNSDHSGS VQGLAPGLPS GSGAEDEEAA GGGCCPDGGG CSRCCCCCAG SGGSAGSGGS GGVAGPGGG GAGSAALCLR LGREQRRYSL WDCLWILAAV AVYFADVGTD VWLAVDYYLR GQRWWFGLTL FFVVLGSLSV Q VFSFRWFV HDFSTEDSAT AAAASSCPQP GADCKTVVGG GSAAGEGEAR PSTPQRQASN ASKSNIAAAN SGSNSSGATR AS GKHRSAS CSFCIWLLQS LIHILQLGQI WRYFHTIYLG IRSRQSGEND RWRFYWKMVY EYADVSMLHL LATFLESAPQ LVL QLCIIV QTHSLQALQG FTAAASLVSL AWALASYQKA LRDSRDDKKP ISYMAVIIQF CWHFFTIAAR VITFALFASV FQLY FGIFI VLHWCIMTFW IVHCETEFCI TKWEEIVFDM VVGIIYIFSW FNVKEGRTRC RLFIYYFVIL LENTALSALW YLYKA PQIA DAFAIPALCV VFSSFLTGVV FMLMYYAFFH PNGPRFGQSP SCACEDPAAA FTLPPDVATS TLRSISNNRS VVSDRD QKF AERDGCVPVF QVRPTAPSTP SSRPPRIEES VIKIDLFRNR YPAWERHVLD RSLRKAILAF ECSPSPPRLQ YKDDALI QE RLEYETTL

UniProtKB: XK-related protein 4

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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

Concentration4 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.28 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 305611
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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