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- PDB-8q30: Sulfolobus acidocaldarius AAP filament. -

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Basic information

Entry
Database: PDB / ID: 8q30
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: 3.22 Å
AuthorsIsupov, M.N. / Gaines, M. / Daum, B. / McLaren, M.
Funding supportEuropean Union, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF4352 domain-containing protein
B: DUF4352 domain-containing protein
C: DUF4352 domain-containing protein
D: DUF4352 domain-containing protein
E: DUF4352 domain-containing protein
F: DUF4352 domain-containing protein
G: DUF4352 domain-containing protein
H: DUF4352 domain-containing protein
I: DUF4352 domain-containing protein
J: DUF4352 domain-containing protein
K: DUF4352 domain-containing protein
L: DUF4352 domain-containing protein
M: DUF4352 domain-containing protein
N: DUF4352 domain-containing protein
O: DUF4352 domain-containing protein
P: DUF4352 domain-containing protein
Q: DUF4352 domain-containing protein
R: DUF4352 domain-containing protein
S: DUF4352 domain-containing protein
T: DUF4352 domain-containing protein
U: DUF4352 domain-containing protein
V: DUF4352 domain-containing protein
W: DUF4352 domain-containing protein
X: DUF4352 domain-containing protein
Y: DUF4352 domain-containing protein
Z: DUF4352 domain-containing protein
a: DUF4352 domain-containing protein
b: DUF4352 domain-containing protein
c: DUF4352 domain-containing protein
d: DUF4352 domain-containing protein
e: DUF4352 domain-containing protein
f: DUF4352 domain-containing protein
g: DUF4352 domain-containing protein
h: DUF4352 domain-containing protein
i: DUF4352 domain-containing protein
j: DUF4352 domain-containing protein
k: DUF4352 domain-containing protein
l: DUF4352 domain-containing protein
m: DUF4352 domain-containing protein
n: DUF4352 domain-containing protein
o: DUF4352 domain-containing protein
p: DUF4352 domain-containing protein
q: DUF4352 domain-containing protein
r: DUF4352 domain-containing protein
s: DUF4352 domain-containing protein
t: DUF4352 domain-containing protein
u: DUF4352 domain-containing protein
v: DUF4352 domain-containing protein
w: DUF4352 domain-containing protein
x: DUF4352 domain-containing protein
y: DUF4352 domain-containing protein
z: DUF4352 domain-containing protein
1: DUF4352 domain-containing protein
2: DUF4352 domain-containing protein
3: DUF4352 domain-containing protein
4: DUF4352 domain-containing protein
5: DUF4352 domain-containing protein
6: DUF4352 domain-containing protein
7: DUF4352 domain-containing protein
8: DUF4352 domain-containing protein
9: DUF4352 domain-containing protein
0: DUF4352 domain-containing protein
LA: DUF4352 domain-containing protein
LB: DUF4352 domain-containing protein
LC: DUF4352 domain-containing protein
LD: DUF4352 domain-containing protein
LE: DUF4352 domain-containing protein
LF: DUF4352 domain-containing protein
LG: DUF4352 domain-containing protein
LH: DUF4352 domain-containing protein
LI: DUF4352 domain-containing protein
LJ: DUF4352 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,108,644288
Polymers1,020,74672
Non-polymers87,899216
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 14177.022 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Source: (natural) Sulfolobus acidocaldarius (acidophilic) / References: UniProt: A0A0U3GLH8
#2: Polysaccharide...
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 96
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide...
6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 650.606 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_6*SO/2=O/2=O]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Glcp6SH]{}}}}LINUCSPDB-CARE
#4: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 42.33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 6272

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Processing

EM softwareName: REFMAC / Version: 5.8.0267 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -39.879 ° / Axial rise/subunit: 15.403 Å / Axial symmetry: C1
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 947729 / 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
RefinementResolution: 3.22→3.22 Å / Cor.coef. Fo:Fc: 0.838 / SU B: 7.068 / SU ML: 0.116 / ESU R: 0.112
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.38727 --
obs0.38727 9846465 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 74.836 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20.17 Å2-0.06 Å2
2---0.09 Å2-0.12 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Total: 77784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.01279512
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.8851.736109728
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.675510080
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.72724.1942232
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.8351510512
ELECTRON MICROSCOPYr_dihedral_angle_4_deg7.81615144
ELECTRON MICROSCOPYr_chiral_restr0.1010.213536
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0256952
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_it5.0356.07340536
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it8.9759.11350544
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it7.2538.7138976
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined20.536299551
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.501 730550 -
obs--100 %

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