[English] 日本語
Yorodumi
- EMDB-19608: Sulfolobus acidocaldarius threads (0406) filament. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19608
TitleSulfolobus acidocaldarius threads (0406) filament.
Map data
Sample
  • Organelle or cellular component: Filament 0406
    • Protein or peptide: Sulfolobus acidocaldarius threads (0406) filament.
  • Ligand: alpha-D-mannopyranose
Keywordscell surface appendage / N-glycosylation / O-glycosylation / PROTEIN FIBRIL
Function / homologyUncharacterized protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
Methodhelical reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsIsupov MN / Gaines M / McLaren M / Daum B
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: Nat Commun / Year: 2024
Title: Towards a molecular picture of the archaeal cell surface.
Authors: Matthew C Gaines / Michail N Isupov / Mathew McLaren / Clara L Mollat / Risat Ul Haque / Jake K Stephenson / Shamphavi Sivabalasarma / Cyril Hanus / Daniel Kattnig / Vicki A M Gold / Sonja ...Authors: Matthew C Gaines / Michail N Isupov / Mathew McLaren / Clara L Mollat / Risat Ul Haque / Jake K Stephenson / Shamphavi Sivabalasarma / Cyril Hanus / Daniel Kattnig / Vicki A M Gold / Sonja Albers / Bertram Daum /
Abstract: Archaea produce various protein filaments with specialised functions. While some archaea produce only one type of filament, the archaeal model species Sulfolobus acidocaldarius generates four. These ...Archaea produce various protein filaments with specialised functions. While some archaea produce only one type of filament, the archaeal model species Sulfolobus acidocaldarius generates four. These include rotary swimming propellers analogous to bacterial flagella (archaella), pili for twitching motility (Aap), adhesive fibres (threads), and filaments facilitating homologous recombination upon UV stress (UV pili). Here, we use cryo-electron microscopy to describe the structure of the S. acidocaldarius archaellum at 2.0 Å resolution, and update the structures of the thread and the Aap pilus at 2.7 Å and 2.6 Å resolution, respectively. We define features unique to archaella of the order Sulfolobales and compare their structure to those of Aap and threads in the context of the S-layer. We define distinct N-glycan patterns in the three filaments and identify a putative O-glycosylation site in the thread. Finally, we ascertain whether N-glycan truncation leads to structural changes in archaella and Aap.
History
DepositionFeb 12, 2024-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19608.png

Downloads & links

-
Map

FileDownload / File: emd_19608.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.224 Å		0.83 Å/pix.
x 256 pix.
= 212.224 Å		0.83 Å/pix.
x 256 pix.
= 212.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.04216582 - 0.15303086
Average (Standard dev.)0.0003740104 (±0.0056573274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.224 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_19608_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19608_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Filament 0406

EntireName: Filament 0406
Components
  • Organelle or cellular component: Filament 0406
    • Protein or peptide: Sulfolobus acidocaldarius threads (0406) filament.
  • Ligand: alpha-D-mannopyranose

-
Supramolecule #1: Filament 0406

SupramoleculeName: Filament 0406 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)

-
Macromolecule #1: Sulfolobus acidocaldarius threads (0406) filament.

MacromoleculeName: Sulfolobus acidocaldarius threads (0406) filament. / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)
Molecular weightTheoretical: 19.720252 KDa
SequenceString:
DVIYYYQGQI TVGNVAPPMY FAIQPNGNAK IGNNSNVPSY INAQPSSGGS GFTAQVNITN ATYNYYFNFM GLAVSKTGYI YLAKVAYSY TATNNPIQNA TLYIMNQQGQ IVYKYKLIVN GVVNSTLPST PLQINSGSYI VSLLIVPYQG TLPKTPSNDL A TITVNFGF SPMTASPPPI PLPSP

UniProtKB: Uncharacterized protein

-
Macromolecule #3: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 3 / Number of copies: 5 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 3
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 20579 / Average exposure time: 2.57 sec. / Average electron dose: 43.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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 reconstructionApplied symmetry - Helical parameters - Δz: 31.65 Å
Applied symmetry - Helical parameters - Δ&Phi: -103.281 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 626078
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-8rzl:
Sulfolobus acidocaldarius threads (0406) filament.

-
Atomic model buiding 2

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8rzl:
Sulfolobus acidocaldarius threads (0406) filament.

+
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