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- PDB-9ets: Sulfolobus acidocaldarius AAP filament -

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Basic information

Entry
Database: PDB / ID: 9ets
TitleSulfolobus acidocaldarius AAP filament
ComponentsDUF4352 domain-containing protein
KeywordsPROTEIN FIBRIL / cell surface appendage / N-glycosylation
Function / homologyImmunoglobulin-like fold / membrane / DUF4352 domain-containing protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 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 26, 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
e: DUF4352 domain-containing protein
h: 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
g: DUF4352 domain-containing protein
j: 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
f: DUF4352 domain-containing protein
i: DUF4352 domain-containing protein
l: DUF4352 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)614,340148
Polymers524,55037
Non-polymers89,790111
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.: 37 / Source method: isolated from a natural source / Source: (natural) Sulfolobus acidocaldarius (acidophilic) / References: UniProt: A0A0U3GLH8
#2: Polysaccharide...
6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6) ...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: 974.887 Da / Num. of mol.: 49
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_6*SO/2=O/2=O][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b3-c1_b4-d1_b6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Glcp6SH]{}[(4+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 37
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide...
6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D- ...6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.: 25
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_b6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Glcp6SH]{}[(6+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
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 / Nominal defocus max: 2100 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.57 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 22790

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPU3.5image acquisition
4cryoSPARC4.4.1CTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
11REFMAC5.8.0267model refinement
15cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -39.86 ° / Axial rise/subunit: 15.52 Å / Axial symmetry: C1
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 505862 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Details: Jligand was used for preparing dictionaries for an unusual sugars
RefinementResolution: 2.6→308.74 Å / Cor.coef. Fo:Fc: 0.861 / SU B: 6.256 / SU ML: 0.118 / ESU R: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.41081 --
obs0.41081 3507019 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 110.218 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20.04 Å20.05 Å2
2---0.7 Å2-0.04 Å2
3---1.53 Å2
Refinement stepCycle: 1 / Total: 42941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01344075
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.9451.82261266
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.91155180
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.27724.1941147
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.798155402
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.4531574
ELECTRON MICROSCOPYr_chiral_restr0.0850.28237
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0229415
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.5279.03120831
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it6.31813.54525974
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it4.66212.84423244
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined15.572163353
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.6 259529 -
obs--100 %

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