[English] 日本語
Yorodumi
- EMDB-13157: Cryo-EM density of caspase-3 cleaved rXKR9 in complex with a sybo... -

+
Open data


ID or keywords:

Loading...

-
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
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
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 / Dutzler R
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-
UpdateAug 25, 2021-
Current statusAug 25, 2021Processing site: PDBe / Status: Released

-
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

-
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

-
Supplemental data

-
Mask #1

Fileemd_13157_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13157_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13157_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 17 KDa

-
Supramolecule #2: rXKR9

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

-
Supramolecule #3: Sybody

SupramoleculeName: Sybody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

-
Image processing

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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more