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- PDB-8rey: Cuniculiplasma divulgatum filament -

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Basic information

Entry
Database: PDB / ID: 8rey
TitleCuniculiplasma divulgatum filament
ComponentsFlagellin-like protein
KeywordsPROTEIN FIBRIL / cell surface appendage / N-glycosylation
Function / homologyArchaeal Type IV pilin, N-terminal / Archaeal Type IV pilin, N-terminal / Flagellin/pilin, N-terminal / membrane / Flagellin-like protein
Function and homology information
Biological speciesCuniculiplasma divulgatum (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsIsupov, M.N. / Gaines, M. / Daum, B. / McLaren, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: ISME J / Year: 2025
Title: Unusual cell surfaces, pili, and archaella of Thermoplasmatales archaea.
Authors: Matthew C Gaines / Michail N Isupov / Mathew McLaren / Risat Ul Haque / Alejandra Recalde / Rafael Bargiela / Vicki A M Gold / Sonja-Verena Albers / Peter N Golyshin / Olga V Golyshina / Bertram Daum /
Abstract: Archaea of the order Thermoplasmatales push the boundaries of our current knowledge of prokaryotic life. They show distinct cellular plasticity, heterogenous cell morphologies, and lack a ...Archaea of the order Thermoplasmatales push the boundaries of our current knowledge of prokaryotic life. They show distinct cellular plasticity, heterogenous cell morphologies, and lack a paracrystalline S-layer. As the S-layer has previously been implicated in acting as a stator scaffold for filaments driving cellular propulsion, particularly archaella, we asked whether the absence of an S-layer precludes the formation of functional archaella or pili in Thermoplasmatales. Using cryoEM, we investigated the two Thermoplasmatales species Cuniculiplasma divulgatum and Oxyplasma meridianum. We found that these species indeed generate pili and archaella and that the latter likely function in cellular propulsion. Whereas C. divulgatum produces pili with terminal hooks using a unique assembly machinery, O. meridianum generates unusually wide, "barbed" archaella with a high degree of glycosylation. Our results show that for the generation of functional archaella and pili, a canonical S-layer is not necessary.
History
DepositionDec 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Oct 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Flagellin-like protein
C: Flagellin-like protein
A: Flagellin-like protein
B: Flagellin-like protein
D: Flagellin-like protein
E: Flagellin-like protein
F: Flagellin-like protein
G: Flagellin-like protein
H: Flagellin-like protein
I: Flagellin-like protein
J: Flagellin-like protein
K: Flagellin-like protein
L: Flagellin-like protein
N: Flagellin-like protein
O: Flagellin-like protein
P: Flagellin-like protein
Q: Flagellin-like protein
R: Flagellin-like protein
S: Flagellin-like protein
T: Flagellin-like protein
U: Flagellin-like protein
V: Flagellin-like protein
W: Flagellin-like protein
X: Flagellin-like protein
Y: Flagellin-like protein
Z: Flagellin-like protein
a: Flagellin-like protein
b: Flagellin-like protein
c: Flagellin-like protein
d: Flagellin-like protein
e: Flagellin-like protein
f: Flagellin-like protein
g: Flagellin-like protein
h: Flagellin-like protein
i: Flagellin-like protein
j: Flagellin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)575,939108
Polymers486,14936
Non-polymers89,79172
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 ...
Flagellin-like protein


Mass: 13504.127 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Cuniculiplasma divulgatum (archaea) / References: UniProt: A0A1N5V6R6
#2: Polysaccharide...
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[D-glycero- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[D-glycero-beta-D-galacto-heptopyranose-(1-2)]6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 1247.091 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[]{[(4+1)][b-D-Galp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Galp6SH]{[(2+1)][b-D-Galp]{}[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(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: Cuniculiplasma divulgatum type IV filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Cuniculiplasma divulgatum (archaea)
Buffer solutionpH: 1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
9REFMAC5.8.0267model refinement
10UCSF ChimeraXmodel refinement
11ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 106.047 ° / Axial rise/subunit: 5.188 Å / Axial symmetry: C1
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 645487 / Symmetry type: HELICAL
RefinementResolution: 2.61→2.61 Å / Cor.coef. Fo:Fc: 0.862 / SU B: 4.838 / SU ML: 0.094 / ESU R: 0.133
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.39763 --
obs0.39763 2982175 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 103.565 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å2-0.01 Å20 Å2
2---1.3 Å2-0 Å2
3---2.61 Å2
Refinement stepCycle: 1 / Total: 40140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01340932
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.5931.83956808
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.74454824
ELECTRON MICROSCOPYr_dihedral_angle_2_deg23.42625792
ELECTRON MICROSCOPYr_dihedral_angle_3_deg9.607155220
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0910.28172
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0224660
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_it2.5878.60219404
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it4.75412.90224192
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it2.86912.04321528
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined13.171150489
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.069 221710 -
obs--100 %

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