[English] 日本語
- PDB-6nav: Cryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6nav
TitleCryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus
KeywordsSTRUCTURAL PROTEIN / helical symmetry / archaeal pilus
Function / homologyintegral component of membrane / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus islandicus LAL14/1 (acidophilic)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang, F. / Cvirkaite-Krupovic, V. / Prangishvili, D. / Krupovic, M. / Egelman, E.H.
Funding support United States, 1items
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 Report
SummaryFull reportAbout validation report
DepositionDec 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-0397
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0397
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
A: M9UD72
B: M9UD72
C: M9UD72
D: M9UD72
E: M9UD72
F: M9UD72
G: M9UD72
H: M9UD72
I: M9UD72
J: M9UD72
K: M9UD72
L: M9UD72
M: M9UD72
N: M9UD72
O: M9UD72
P: M9UD72
Q: M9UD72
R: M9UD72
S: M9UD72
T: M9UD72
U: M9UD72

Theoretical massNumber of molelcules
Total (without water)266,30921

  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein ...

Mass: 12681.375 Da / Num. of mol.: 21 / Source method: isolated from a natural source
Source: (natural) Sulfolobus islandicus LAL14/1 (acidophilic)
References: UniProt: M9UD72

Experimental details


EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

Sample preparation

ComponentName: Sulfolobus islandicus LAL14/1 Pilus / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sulfolobus islandicus LAL14/1 (acidophilic)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 90 %

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
Image recordingAverage exposure time: 2 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
Details: Images were stored containing 24 fractions, where each fraction corresponded to a dose of ~2 electrons per Angstrom^2.


SoftwareName: PHENIX / Version: dev_2919: / Classification: refinement
EM software
1EMAN2particle selection
2EPUimage acquisition
4GctfCTF correction
12SPIDER3D reconstruction
13RELION3D reconstruction
14Rosettamodel refinement
15PHENIXmodel refinement
16Cootmodel refinement
Helical symmertyAngular rotation/subunit: 104.97 ° / Axial rise/subunit: 4.94 Å / Axial symmetry: C1
3D reconstructionResolution: 4.1 Å / Resolution method: OTHER / Num. of particles: 181070 / Details: MODEL:MAP FSC, D99 / Symmetry type: HELICAL

About Yorodumi


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


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