[English] 日本語
Yorodumi
- EMDB-0397: Cryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0397
TitleCryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus
Map data
SampleSulfolobus islandicus LAL14/1 Pilus:
M9UD72
Function / homologyintegral component of membrane / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus islandicus LAL14/1 (acidophilic)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang F / Cvirkaite-Krupovic V / Prangishvili D / Krupovic M / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Nat Microbiol / Year: 2019
Title: An extensively glycosylated archaeal pilus survives extreme conditions.
Authors: Fengbin Wang / Virginija Cvirkaite-Krupovic / Mark A B Kreutzberger / Zhangli Su / Guilherme A P de Oliveira / Tomasz Osinski / Nicholas Sherman / Frank DiMaio / Joseph S Wall / David ...Authors: Fengbin Wang / Virginija Cvirkaite-Krupovic / Mark A B Kreutzberger / Zhangli Su / Guilherme A P de Oliveira / Tomasz Osinski / Nicholas Sherman / Frank DiMaio / Joseph S Wall / David Prangishvili / Mart Krupovic / Edward H Egelman /
Abstract: Pili on the surface of Sulfolobus islandicus are used for many functions, and serve as receptors for certain archaeal viruses. The cells grow optimally at pH 3 and ~80 °C, exposing these ...Pili on the surface of Sulfolobus islandicus are used for many functions, and serve as receptors for certain archaeal viruses. The cells grow optimally at pH 3 and ~80 °C, exposing these extracellular appendages to a very harsh environment. The pili, when removed from cells, resist digestion by trypsin or pepsin, and survive boiling in sodium dodecyl sulfate or 5 M guanidine hydrochloride. We used electron cryo-microscopy to determine the structure of these filaments at 4.1 Å resolution. An atomic model was built by combining the electron density map with bioinformatics without previous knowledge of the pilin sequence-an approach that should prove useful for assemblies where all of the components are not known. The atomic structure of the pilus was unusual, with almost one-third of the residues being either threonine or serine, and with many hydrophobic surface residues. While the map showed extra density consistent with glycosylation for only three residues, mass measurements suggested extensive glycosylation. We propose that this extensive glycosylation renders these filaments soluble and provides the remarkable structural stability. We also show that the overall fold of the archaeal pilin is remarkably similar to that of archaeal flagellin, establishing common evolutionary origins.
Validation ReportPDB-ID: 6nav

SummaryFull reportAbout validation report
History
DepositionDec 6, 2018-
Header (metadata) releaseJan 23, 2019-
Map releaseMay 8, 2019-
UpdateJan 8, 2020-
Current statusJan 8, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6nav
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nav
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0397.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 384 pix.
= 537.6 Å
1.4 Å/pix.
x 384 pix.
= 537.6 Å
1.4 Å/pix.
x 384 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.127 / Movie #1: 0.127
Minimum - Maximum-0.15029839 - 0.3493753
Average (Standard dev.)0.00035732737 (±0.0065073087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-0.1500.3490.000

-
Supplemental data

-
Sample components

-
Entire Sulfolobus islandicus LAL14/1 Pilus

EntireName: Sulfolobus islandicus LAL14/1 Pilus / Number of components: 2

-
Component #1: protein, Sulfolobus islandicus LAL14/1 Pilus

ProteinName: Sulfolobus islandicus LAL14/1 Pilus / Recombinant expression: No
SourceSpecies: Sulfolobus islandicus LAL14/1 (acidophilic)

-
Component #2: protein, M9UD72

ProteinName: M9UD72 / Number of Copies: 21 / Recombinant expression: No
MassTheoretical: 12.681375 kDa
SourceSpecies: Sulfolobus islandicus LAL14/1 (acidophilic)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4.94 Å / Delta phi: 104.97 %deg;
Sample solutionpH: 6
VitrificationCryogen name: ETHANE / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image acquisition

Image acquisitionDetails: Images were stored containing 24 fractions, where each fraction corresponded to a dose of ~2 electrons per Angstrom^2.

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: SPIDER, RELION / Resolution: 4.1 Å / Resolution method: OTHER / Details: MODEL:MAP FSC, D99

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

Read more

-
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.

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