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- PDB-7pnb: Sulfolobus acidocaldarius 0406 filament. -

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Basic information

Entry
Database: PDB / ID: 7pnb
TitleSulfolobus acidocaldarius 0406 filament.
ComponentsSulfolobus acidocaldarius 0406 filament.
KeywordsPROTEIN FIBRIL / cell surface appendage / beta-strand addition / isopeptide bond / N-glycosylation / beta-sandwich
Function / homologyUncharacterized protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsIsupov, M.N. / Gaines, M. / Daum, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: Nat Commun / Year: 2022
Title: Electron cryo-microscopy reveals the structure of the archaeal thread filament.
Authors: Matthew C Gaines / Michail N Isupov / Shamphavi Sivabalasarma / Risat Ul Haque / Mathew McLaren / Clara L Mollat / Patrick Tripp / Alexander Neuhaus / Vicki A M Gold / Sonja-Verena Albers / Bertram Daum /
Abstract: Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal ...Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.
History
DepositionSep 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfolobus acidocaldarius 0406 filament.
B: Sulfolobus acidocaldarius 0406 filament.
C: Sulfolobus acidocaldarius 0406 filament.
D: Sulfolobus acidocaldarius 0406 filament.
E: Sulfolobus acidocaldarius 0406 filament.
F: Sulfolobus acidocaldarius 0406 filament.
G: Sulfolobus acidocaldarius 0406 filament.
H: Sulfolobus acidocaldarius 0406 filament.
I: Sulfolobus acidocaldarius 0406 filament.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,87254
Polymers200,6249
Non-polymers48,24845
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area88960 Å2
ΔGint447 kcal/mol
Surface area79360 Å2

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Components

#1: Protein
Sulfolobus acidocaldarius 0406 filament.


Mass: 22291.539 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ATZ20_07285 / Production host: Sulfolobus acidocaldarius (acidophilic) / References: UniProt: A0A0U2Y8S3
#2: Polysaccharide...
beta-D-glucopyranose-(1-4)-6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)] ...beta-D-glucopyranose-(1-4)-6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1137.028 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_6*SO/2=O/2=O][a2122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-4-4/a4-b1_b3-c1_b4-e1_b6-f1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Glcp6SH]{[(4+1)][b-D-Glcp]{}}[(4+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D- ...6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 812.746 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_6*SO/2=O/2=O][a1122h-1a_1-5]/1-1-2-3/a4-b1_b3-c1_b4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Glcp6SH]{}[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)
Buffer solutionpH: 3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Mixed population of filaments isolated from Sulfolobus acidocaldarius
VitrificationCryogen name: ETHANE

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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 FIELD
Image recordingElectron dose: 42.33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6272

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC3.2.0particle selectioncryoSPARC filament tracer was used to automatically pick particles
4cryoSPARC3.2.0CTF correction
7Cootmodel fitting
8UCSF Chimeramodel fitting
9UCSF ChimeraXmodel fitting
10MOLREPmodel fitting
12REFMACmodel refinement
13CCP4 packagemodel refinement
14cryoSPARC3.2.0initial Euler assignment
15cryoSPARC3.2.0final Euler assignment
16cryoSPARC3.2.0classification
17cryoSPARC3.2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -103.234 ° / Axial rise/subunit: 31.649 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 410270
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188620 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Details: Jligand was used for preparing dictionaries for an unusual sugars and an isopeptide link beween main chain nitrogen of the N-terminal D25 and C gamma of N57 from N-2 monomer in the filament.

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