[English] 日本語
Yorodumi
- PDB-8xej: Cryo-EM structure of human XKR8-basigin complex in lipid nanodisc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xej
TitleCryo-EM structure of human XKR8-basigin complex in lipid nanodisc
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Isoform 2 of Basigin
  • XK-related protein 8
KeywordsLIPID TRANSPORT / scramblase / apoptosis / membrane protein
Function / homology
Function and homology information


tolerance induction to self antigen / Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / phosphatidylserine exposure on apoptotic cell surface / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / phospholipid scramblase activity / neutrophil clearance / response to mercury ion / engulfment of apoptotic cell ...tolerance induction to self antigen / Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / phosphatidylserine exposure on apoptotic cell surface / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / phospholipid scramblase activity / neutrophil clearance / response to mercury ion / engulfment of apoptotic cell / neural retina development / endothelial tube morphogenesis / Pyruvate metabolism / apoptotic process involved in development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / mannose binding / decidualization / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / positive regulation of myoblast differentiation / Integrin cell surface interactions / embryo implantation / response to cAMP / photoreceptor inner segment / Degradation of the extracellular matrix / neutrophil chemotaxis / positive regulation of endothelial cell migration / establishment of localization in cell / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / virus receptor activity / signaling receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / 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 / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Basigin / XK-related protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsSakuragi, T.S. / Kanai, R.K. / Kikkawa, M.K. / Toyoshima, C.T. / Nagata, S.N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K06102 Japan
Japan Society for the Promotion of Science (JSPS)A21H04770 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121002 Japan
CitationJournal: J Biol Chem / Year: 2024
Title: The role of the C-terminal tail region as a plug to regulate XKR8 lipid scramblase.
Authors: Takaharu Sakuragi / Ryuta Kanai / Mayumi Otani / Masahide Kikkawa / Chikashi Toyoshima / Shigekazu Nagata /
Abstract: XK-related 8 (XKR8), in complex with the transmembrane glycoprotein basigin, functions as a phospholipid scramblase activated by the caspase-mediated cleavage or phosphorylation of its C-terminal ...XK-related 8 (XKR8), in complex with the transmembrane glycoprotein basigin, functions as a phospholipid scramblase activated by the caspase-mediated cleavage or phosphorylation of its C-terminal tail. It carries a putative phospholipid translocation path of multiple hydrophobic and charged residues in the transmembrane region. It also has a crucial tryptophan at the exoplasmic end of the path that regulates its scrambling activity. We herein investigated the tertiary structure of the human XKR8-basigin complex embedded in lipid nanodiscs at an overall resolution of 3.66 Å. We found that the C-terminal tail engaged in intricate polar and van der Waals interactions with a groove at the cytoplasmic surface of XKR8. These interactions maintained the inactive state of XKR8. Point mutations to disrupt these interactions strongly enhanced the scrambling activity of XKR8, suggesting that the activation of XKR8 is mediated by releasing the C-terminal tail from the cytoplasmic groove. We speculate that the cytoplasmic tail region of XKR8 functions as a plug to prevent the scrambling of phospholipids.
History
DepositionDec 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Isoform 2 of Basigin
X: XK-related protein 8
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4825
Polymers111,7004
Non-polymers7821
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Co-immunoprecipitation assay confirmed the assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Isoform 2 of Basigin / 5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / ...5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / Hepatoma-associated antigen / HAb18G / Leukocyte activation antigen M6 / OK blood group antigen / Tumor cell-derived collagenase stimulatory factor / TCSF


Mass: 19592.814 Da / Num. of mol.: 1 / Mutation: N152Q, N186Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BSG / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35613
#2: Protein XK-related protein 8 / hXkr8


Mass: 45975.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XKR8, XRG8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H6D3
#3: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 22869.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#4: Antibody Fab light chain / Fragment antigen-binding


Mass: 23261.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#5: Chemical ChemComp-DLP / 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DI-LINOLEOYL-3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 782.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1human XKR8-basigin complex bound to Fab fragment in lipid nanodiscCOMPLEX#1-#40MULTIPLE SOURCES
2human XKR8-basigin complexCOMPLEX#1-#21RECOMBINANT
3Fab fragmentFragment antigen-bindingCOMPLEX#3-#41RECOMBINANT
Molecular weightValue: 0.11 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Oryctolagus cuniculus (rabbit)9986
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Homo sapiens (human)9606
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162528 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047343
ELECTRON MICROSCOPYf_angle_d0.78910011
ELECTRON MICROSCOPYf_dihedral_angle_d13.4012587
ELECTRON MICROSCOPYf_chiral_restr0.0441140
ELECTRON MICROSCOPYf_plane_restr0.0082146

+
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