[English] 日本語
Yorodumi
- EMDB-51935: Ex vivo cannulae fiber structure of Pyrodictium abyssi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51935
TitleEx vivo cannulae fiber structure of Pyrodictium abyssi
Map data
Sample
  • Complex: Ex vivo CanX fibers from Pyrodictium abyssi
    • Protein or peptide: CanX
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNanotube Archaea Helical protein fiber DNA-binding / PROTEIN FIBRIL
Biological speciesPyrodictium abyssi DSM 6158 (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsSleutel M / Remaut H
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G043021N Belgium
CitationJournal: bioRxiv / Year: 2024
Title: Donor Strand Complementation and Calcium Ion Coordination Drive the Chaperone-free Polymerization of Archaeal Cannulae.
Authors: Mike Sleutel / Ravi R Sonani / Jessalyn G Miller / Fengbin Wang / Andres Gonzalez Socorro / Yang Chen / Reece Martin / Borries Demeler / Michael J Rudolph / Vikram Alva / Han Remaut / Edward ...Authors: Mike Sleutel / Ravi R Sonani / Jessalyn G Miller / Fengbin Wang / Andres Gonzalez Socorro / Yang Chen / Reece Martin / Borries Demeler / Michael J Rudolph / Vikram Alva / Han Remaut / Edward H Egelman / Vincent P Conticello /
Abstract: Cannulae are tubular protein filaments that accumulate on the extracellular surface of the hyperthermophilic archaeon during cell division. Cannulae have been postulated to act as a primitive ...Cannulae are tubular protein filaments that accumulate on the extracellular surface of the hyperthermophilic archaeon during cell division. Cannulae have been postulated to act as a primitive extracellular matrix through which cells could communicate or exchange material, although their native biological function remains obscure. Here, we report cryoEM structural analyses of cannulae and of protein assemblies derived from recombinant cannula-like proteins. Three-dimensional reconstructions of cannulae revealed that the structural interactions between protomers in the native and recombinant filaments were based on donor strand complementation, a form of non-covalent polymerization in which a donor β-strand from one subunit is inserted into an acceptor groove in a β-sheet of a neighboring subunit. Donor strand complementation in cannulae is reinforced through calcium ion coordination at the interfaces between structural subunits in the respective assemblies. While donor strand complementation occurs during the assembly of chaperone-usher pili, this process requires the participation of accessory proteins that are localized in the outer membrane. In contrast, we demonstrate that calcium ions can induce assembly of cannulae in the absence of other co-factors. Crystallographic analysis of a recombinant cannula-like protein monomer provided evidence that calcium ion binding primes the precursor for donor strand invasion through unblocking of the acceptor groove. Bioinformatic analysis suggested that structurally homologous cannula-like proteins occurred within the genomes of other hyperthermophilic archaea and were encompassed within the TasA superfamily of biomatrix proteins. CryoEM structural analyses of tubular filaments derived from assembly of a recombinant cannula-like protein from an uncultured species revealed a common mode of assembly to the cannulae, in which donor strand complementation and calcium ion binding stabilized longitudinal and lateral assembly in tubular 2D sheets.
History
DepositionOct 28, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51935.png

Downloads & links

-
Map

FileDownload / File: emd_51935.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 600 pix.
= 426. Å		0.71 Å/pix.
x 600 pix.
= 426. Å		0.71 Å/pix.
x 600 pix.
= 426. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0691
Minimum - Maximum-0.13294679 - 0.32972667
Average (Standard dev.)0.00158073 (±0.014079615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 426.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51935_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51935_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51935_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ex vivo CanX fibers from Pyrodictium abyssi

EntireName: Ex vivo CanX fibers from Pyrodictium abyssi
Components
  • Complex: Ex vivo CanX fibers from Pyrodictium abyssi
    • Protein or peptide: CanX
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Ex vivo CanX fibers from Pyrodictium abyssi

SupramoleculeName: Ex vivo CanX fibers from Pyrodictium abyssi / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrodictium abyssi DSM 6158 (archaea)

-
Macromolecule #1: CanX

MacromoleculeName: CanX / type: protein_or_peptide / ID: 1 / Number of copies: 154 / Enantiomer: LEVO
Source (natural)Organism: Pyrodictium abyssi DSM 6158 (archaea)
Molecular weightTheoretical: 18.745406 KDa
Recombinant expressionOrganism: Pyrodictium abyssi DSM 6158 (archaea)
SequenceString:
MRYTTLAIAG IIASAAALAL LAGFATTQSP LNSFYATGTA QAVQEPIDVE SHLDNTIAPA AGAQGYKDMG YVKIINYTDV NVVKLKVTL ANAAQLRPYF KYLQLVLTSN ASSTVEETKA VLSLKKPSAV IILDNDDYSS TNKIQLKVEA YYEAKEGMLF D SLPVILNF QVLSVS

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 462 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 154 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 5.5
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.178 Å
Applied symmetry - Helical parameters - Δ&Phi: 12.094 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 310172
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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://pdbjlvh1.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