[English] 日本語
Yorodumi
- EMDB-0088: XaxAB pore complex from Xenorhabdus nematophila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0088
TitleXaxAB pore complex from Xenorhabdus nematophila
Map data
Sample
  • Complex: XaxAB complex (13 XaxA + 13 XaxB)
    • Complex: XaxA protomer
      • Protein or peptide: XaxA
    • Complex: XaxB protomer
      • Protein or peptide: XaxB
Keywordsbacterial toxin / pore forming-toxins / TOXIN
Function / homology: / membrane / XaxA / XaxB
Function and homology information
Biological speciesXenorhabdus nematophila ATCC 19061 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSchubert E / Vetter IR / Prumbaum D / Penczek PA / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Elife / Year: 2018
Title: Membrane insertion of α-xenorhabdolysin in near-atomic detail.
Authors: Evelyn Schubert / Ingrid R Vetter / Daniel Prumbaum / Pawel A Penczek / Stefan Raunser /
Abstract: α-Xenorhabdolysins (Xax) are α-pore-forming toxins (α-PFT) that form 1-1.3 MDa large pore complexes to perforate the host cell membrane. PFTs are used by a variety of bacterial pathogens to attack ...α-Xenorhabdolysins (Xax) are α-pore-forming toxins (α-PFT) that form 1-1.3 MDa large pore complexes to perforate the host cell membrane. PFTs are used by a variety of bacterial pathogens to attack host cells. Due to the lack of structural information, the molecular mechanism of action of Xax toxins is poorly understood. Here, we report the cryo-EM structure of the XaxAB pore complex from and the crystal structures of the soluble monomers of XaxA and XaxB. The structures reveal that XaxA and XaxB are built similarly and appear as heterodimers in the 12-15 subunits containing pore, classifying XaxAB as bi-component α-PFT. Major conformational changes in XaxB, including the swinging out of an amphipathic helix are responsible for membrane insertion. XaxA acts as an activator and stabilizer for XaxB that forms the actual transmembrane pore. Based on our results, we propose a novel structural model for the mechanism of Xax intoxication.
History
DepositionJun 28, 2018-
Header (metadata) releaseJul 25, 2018-
Map releaseJul 25, 2018-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0088.png

Downloads & links

-
Map

FileDownload / File: emd_0088.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 352 pix.
= 390.72 Å		1.11 Å/pix.
x 352 pix.
= 390.72 Å		1.11 Å/pix.
x 352 pix.
= 390.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0192
Minimum - Maximum-0.032193013 - 0.08761053
Average (Standard dev.)0.00048514162 (±0.0037814577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 390.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : XaxAB complex (13 XaxA + 13 XaxB)

EntireName: XaxAB complex (13 XaxA + 13 XaxB)
Components
  • Complex: XaxAB complex (13 XaxA + 13 XaxB)
    • Complex: XaxA protomer
      • Protein or peptide: XaxA
    • Complex: XaxB protomer
      • Protein or peptide: XaxB

-
Supramolecule #1: XaxAB complex (13 XaxA + 13 XaxB)

SupramoleculeName: XaxAB complex (13 XaxA + 13 XaxB) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenorhabdus nematophila ATCC 19061 (bacteria)

-
Supramolecule #2: XaxA protomer

SupramoleculeName: XaxA protomer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: 13 XaxA protomers in the XaxAB pore complex
Source (natural)Organism: Xenorhabdus nematophila ATCC 19061 (bacteria)

-
Supramolecule #3: XaxB protomer

SupramoleculeName: XaxB protomer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: 13 XaxB protomers in the XaxAB pore complex
Source (natural)Organism: Xenorhabdus nematophila ATCC 19061 (bacteria)

-
Macromolecule #1: XaxA

MacromoleculeName: XaxA / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Xenorhabdus nematophila ATCC 19061 (bacteria)
Molecular weightTheoretical: 47.465859 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MENDMSSNQT LAEKKIPVSE VPSATLKMLT SQAEGVARPG GIFTKGDLIN IKLYVKHSLE LPFTLEGVKE YIGYNDIDID GLKPAKMAT LFKEIHDHAL SWSGVESKVQ QQSIDLENAG KQITLTGDEI ISVIDQMPII ERVKNKLGDL TDKQLAEITY T NDDKEIAV ...String:
MENDMSSNQT LAEKKIPVSE VPSATLKMLT SQAEGVARPG GIFTKGDLIN IKLYVKHSLE LPFTLEGVKE YIGYNDIDID GLKPAKMAT LFKEIHDHAL SWSGVESKVQ QQSIDLENAG KQITLTGDEI ISVIDQMPII ERVKNKLGDL TDKQLAEITY T NDDKEIAV ELGNILESMK KDIKRQQENT QKVKTAVSDF KLKLIGGELS DGTIAQGLQP QISSKKKLMD DNNLSTTIKD LQ SKIDEKN KEIDQFQKDY NKYVGLAFSG MVGGIISWAI TGGIFGDKAE KARKQKNKLI DEVKDLQSQV KDKSALQTSV QNL SLSFAG IHTSMVDAEE ALNHLDFMWN TMLTQITTSR DKFDDINDAL KLTSFVIAFK QVIEPWRDVQ GSAAQLIQTF DEAL AEYKK LYHGTLEVLF QGPHHHHHH

UniProtKB: XaxA

-
Macromolecule #2: XaxB

MacromoleculeName: XaxB / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Xenorhabdus nematophila ATCC 19061 (bacteria)
Molecular weightTheoretical: 38.518688 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: YPEINIKAMN QAVNTIWLLA QRQTSGIEII NDKVKRISAY SREFDEMMRD SLAQLAPVLK QLTSDAAFQT IAQIDEALAD PSLSKDDRE ALTLERNNLI QNLSKHIDNV IVSFTGRTSK LTNKISDISD MVIAERLQDL VTQTESQKTE LQSDIDPKTE K RNKLDADR ...String:
YPEINIKAMN QAVNTIWLLA QRQTSGIEII NDKVKRISAY SREFDEMMRD SLAQLAPVLK QLTSDAAFQT IAQIDEALAD PSLSKDDRE ALTLERNNLI QNLSKHIDNV IVSFTGRTSK LTNKISDISD MVIAERLQDL VTQTESQKTE LQSDIDPKTE K RNKLDADR EKIIESQDVI RQNNIADMFK DFIPSAKDID GLDFTQPKKE AIKQAIKQGA EIARKILGKV SEGLKYIDLA DA RMKLSDQ IDQLITETDE LKAKIREVEL RLSGLKDVMQ IDTERTTLLT EAVKIEQVWI SFAEQLHKLS NDEINQQDLS NLI NGQLDF LNNLTLQYNK LK

UniProtKB: XaxB

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: C-flat-2/1
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298.15 K / Instrument: GATAN CRYOPLUNGE 3

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 43305
Initial angle assignmentType: NOT APPLICABLE / Software - Name: SPHIRE / Software - details: RVIPER
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE / Software - details: MERIDIEN
Final 3D classificationSoftware - Name: SPHIRE / Software - details: ISAC

+
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