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- EMDB-13157: Cryo-EM density of caspase-3 cleaved rXKR9 in complex with a sybo... -

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Basic information

Entry
Database: EMDB / ID: EMD-13157
TitleCryo-EM density of caspase-3 cleaved rXKR9 in complex with a sybody at 4.3A
Map data
Sample
  • Complex: caspase-3 cleaved rXKR9 with sybody
    • Complex: rXKR9
      • Protein or peptide: XK-related protein
    • Complex: Sybody
      • Protein or peptide: Sybody
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
Keywordssmall membrane protein / in complex with sybody / apoptotic lipid scrambling / MEMBRANE PROTEIN
Function / homologyXK-related protein / : / XK-related protein / membrane / plasma membrane / XK-related protein
Function and homology information
Biological speciesRattus norvegicus (Norway rat) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsStraub MS / Sawicka M
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)339116 Switzerland
University of ZurichFK-20-040 Switzerland
CitationJournal: Elife / Year: 2021
Title: Cryo-EM structures of the caspase-activated protein XKR9 involved in apoptotic lipid scrambling.
Authors: Monique S Straub / Carolina Alvadia / Marta Sawicka / Raimund Dutzler /
Abstract: The exposure of the negatively charged lipid phosphatidylserine on the cell surface, catalyzed by lipid scramblases, is an important signal for the clearance of apoptotic cells by macrophages. The ...The exposure of the negatively charged lipid phosphatidylserine on the cell surface, catalyzed by lipid scramblases, is an important signal for the clearance of apoptotic cells by macrophages. The protein XKR9 is a member of a conserved family that has been associated with apoptotic lipid scrambling. Here, we describe structures of full-length and caspase-treated XKR9 from in complex with a synthetic nanobody determined by cryo-electron microscopy. The 43 kDa monomeric membrane protein can be divided into two structurally related repeats, each containing four membrane-spanning segments and a helix that is partly inserted into the lipid bilayer. In the full-length protein, the C-terminus interacts with a hydrophobic pocket located at the intracellular side acting as an inhibitor of protein function. Cleavage by caspase-3 at a specific site releases 16 residues of the C-terminus, thus making the pocket accessible to the cytoplasm. Collectively, the work has revealed the unknown architecture of the XKR family and has provided initial insight into its activation by caspases.
History
DepositionJul 1, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.946
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.946
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7p16
  • Surface level: 0.946
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13157.png

Downloads & links

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Map

FileDownload / File: emd_13157.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 180 pix.
= 234.36 Å		1.3 Å/pix.
x 180 pix.
= 234.36 Å		1.3 Å/pix.
x 180 pix.
= 234.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.946 / Movie #1: 0.946
Minimum - Maximum-4.6579547 - 6.1774025
Average (Standard dev.)0.0026762118 (±0.09859215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 234.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3021.3021.302
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z234.360234.360234.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ332332332
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-4.6586.1770.003

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Supplemental data

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Mask #1

Fileemd_13157_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13157_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13157_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : caspase-3 cleaved rXKR9 with sybody

EntireName: caspase-3 cleaved rXKR9 with sybody
Components
  • Complex: caspase-3 cleaved rXKR9 with sybody
    • Complex: rXKR9
      • Protein or peptide: XK-related protein
    • Complex: Sybody
      • Protein or peptide: Sybody
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE

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Supramolecule #1: caspase-3 cleaved rXKR9 with sybody

SupramoleculeName: caspase-3 cleaved rXKR9 with sybody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 17 KDa

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Supramolecule #2: rXKR9

SupramoleculeName: rXKR9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: Sybody

SupramoleculeName: Sybody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: XK-related protein

MacromoleculeName: XK-related protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 43.563059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKYTICNFMM SVLGIIIYVT DLVADIVLTV RYFYDGQYVF GVLTLSFVLC GTLIVHCFSY SWLKDDLKKA GGENEHYFLL LHCLQGGVF TRYWFVLRTG YHVVFKHSHR TSNFMEEQTD PHKEAIDMAT DLSMLRLFET YLEGCPQLIL QLYAFLERGQ A NFSQYMVI ...String:
MKYTICNFMM SVLGIIIYVT DLVADIVLTV RYFYDGQYVF GVLTLSFVLC GTLIVHCFSY SWLKDDLKKA GGENEHYFLL LHCLQGGVF TRYWFVLRTG YHVVFKHSHR TSNFMEEQTD PHKEAIDMAT DLSMLRLFET YLEGCPQLIL QLYAFLERGQ A NFSQYMVI MVSCCAISWS TVDYQIALRK SLPDKNLLRG FWPKLTYLFY KLFTLLSWML SVVLLLFVDV RTVLLLLLFL WT VGFIWAF INHTQFCNSL SMEFLYRLVV GFILVFTFFN IKGQNTKCPM SCYYTVRVLG TLGILTVFWI YPLSIFNSDY FIP ISATIV LSLLFGIIFL GVYYGTYHPN INAGTQHDEP DGKAPQRDCR IRYFLMDA

UniProtKB: XK-related protein

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Macromolecule #2: Sybody

MacromoleculeName: Sybody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.675293 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
SQVQLVESGG GSVQAGGSLR LSCAASGNIA DIYYLGWFRQ APGKEREGVA ALITYNGRTY YADSVKGRFT VSLDNAKNTV YLQMNSLKP EDTALYYCAA AYNGLIAAPL KVTRYWYWGQ GTQVTVS

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Macromolecule #3: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / 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

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
25.0 mMHEPESHEPES
0.01 %LMNGLauryl Maltose Neopentyl Glycol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 14929 / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 444358
Initial angle assignmentType: OTHER / Details: cryoSPARC
Final angle assignmentType: OTHER / Details: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7p16:
Structure of caspase-3 cleaved rXKR9 in complex with a sybody at 4.3A

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