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- EMDB-18119: Sulfolobus acidocaldarius AAP filament. -

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Basic information

Entry
Database: EMDB / ID: EMD-18119
TitleSulfolobus acidocaldarius AAP filament.
Map data
Sample
  • Organelle or cellular component: Filament
    • Protein or peptide: DUF4352 domain-containing protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscell surface appendage / N-glycosylation / PROTEIN FIBRIL
Function / homologyImmunoglobulin-like fold / membrane / DUF4352 domain-containing protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
Methodhelical reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsIsupov MN / Gaines M / Daum B / McLaren M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: Nat Commun / Year: 2024
Title: CryoEM reveals the structure of an archaeal pilus involved in twitching motility.
Authors: Matthew C Gaines / Shamphavi Sivabalasarma / Michail N Isupov / Risat Ul Haque / Mathew McLaren / Cyril Hanus / Vicki A M Gold / Sonja-Verena Albers / Bertram Daum /
Abstract: Amongst the major types of archaeal filaments, several have been shown to closely resemble bacterial homologues of the Type IV pili (T4P). Within Sulfolobales, member species encode for three types ...Amongst the major types of archaeal filaments, several have been shown to closely resemble bacterial homologues of the Type IV pili (T4P). Within Sulfolobales, member species encode for three types of T4P, namely the archaellum, the UV-inducible pilus system (Ups) and the archaeal adhesive pilus (Aap). Whereas the archaellum functions primarily in swimming motility, and the Ups in UV-induced cell aggregation and DNA-exchange, the Aap plays an important role in adhesion and twitching motility. Here, we present a cryoEM structure of the Aap of the archaeal model organism Sulfolobus acidocaldarius. We identify the component subunit as AapB and find that while its structure follows the canonical T4P blueprint, it adopts three distinct conformations within the pilus. The tri-conformer Aap structure that we describe challenges our current understanding of pilus structure and sheds new light on the principles of twitching motility.
History
DepositionAug 3, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18119.png

Downloads & links

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Map

FileDownload / File: emd_18119.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.047 Å
Density
Contour LevelBy AUTHOR: 0.59
Minimum - Maximum-0.7996451 - 1.8750216
Average (Standard dev.)0.004505234 (±0.05043028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 536.064 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_18119_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18119_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DeepEMhance map

Fileemd_18119_half_map_2.map
AnnotationDeepEMhance map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Filament

EntireName: Filament
Components
  • Organelle or cellular component: Filament
    • Protein or peptide: DUF4352 domain-containing protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Filament

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

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Macromolecule #1: DUF4352 domain-containing protein

MacromoleculeName: DUF4352 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 72 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)
Molecular weightTheoretical: 14.177022 KDa
SequenceString:
LSGAIVALIL VIAGVIIAIA VVLFAFGLIP GISNQGSIQV LGSGTITNST ASGSSRTIYN ITITVKNTGT TSISVTSINI NGQPFNING TAPSIPAGRT QPITFEVTPA SGKPNFSPGA SYTATIYFSN GQGAPATLIY QG

UniProtKB: DUF4352 domain-containing protein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 72 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 3
VitrificationCryogen name: ETHANE
DetailsMixed population of filaments isolated from Sulfolobus acidocaldarius

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 6272 / Average electron dose: 42.33 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 15.403 Å
Applied symmetry - Helical parameters - Δ&Phi: -39.879 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 947729
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsJligand was used for preparing dictionaries for an unusual sugars
RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-8q30:
Sulfolobus acidocaldarius AAP filament.

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