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- PDB-9ev0: Structure of the AAP filament of Sulfolobus acidocaldarius strain... -

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Basic information

Entry
Database: PDB / ID: 9ev0
TitleStructure of the AAP filament of Sulfolobus acidocaldarius strain MW039 (delta agl3 mutant).
ComponentsDUF4352 domain-containing protein
KeywordsPROTEIN FIBRIL / cell surface appendage / N-glycosylation / mutagenesis
Function / homologyImmunoglobulin-like fold / membrane / DUF4352 domain-containing protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsDaum, B. / Isupov, M.N. / Gaines, M. / McLaren, M. / Mollat, C.
Funding supportEuropean Union, 1items
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
DepositionMar 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: DUF4352 domain-containing protein
A: DUF4352 domain-containing protein
D: DUF4352 domain-containing protein
J: DUF4352 domain-containing protein
M: DUF4352 domain-containing protein
P: DUF4352 domain-containing protein
S: DUF4352 domain-containing protein
V: DUF4352 domain-containing protein
Y: DUF4352 domain-containing protein
b: DUF4352 domain-containing protein
H: DUF4352 domain-containing protein
B: DUF4352 domain-containing protein
E: DUF4352 domain-containing protein
K: DUF4352 domain-containing protein
N: DUF4352 domain-containing protein
Q: DUF4352 domain-containing protein
T: DUF4352 domain-containing protein
W: DUF4352 domain-containing protein
Z: DUF4352 domain-containing protein
c: DUF4352 domain-containing protein
I: DUF4352 domain-containing protein
C: DUF4352 domain-containing protein
F: DUF4352 domain-containing protein
L: DUF4352 domain-containing protein
O: DUF4352 domain-containing protein
R: DUF4352 domain-containing protein
U: DUF4352 domain-containing protein
X: DUF4352 domain-containing protein
a: DUF4352 domain-containing protein
d: DUF4352 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,099120
Polymers425,31130
Non-polymers52,78990
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
DUF4352 domain-containing protein


Mass: 14177.022 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Sulfolobus acidocaldarius (acidophilic) / References: UniProt: A0A0U3GLH8
#2: Polysaccharide...
alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 90 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-6DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
Has ligand of interestN
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: Aap filament of the S. acidocaldarius species deficient in sulfoquinovose transferase enzyme
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
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 deficient in agl3 - UDP-sulfoquinovose synthase
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 / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.5 sec. / Electron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of real images: 29189

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Processing

EM software
IDNameVersionCategory
2REFMAC5.8.0267model refinement
3EPU3.5image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -39.953 ° / Axial rise/subunit: 15.282 Å / Axial symmetry: C1
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 691479 / Symmetry type: HELICAL

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