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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: To Be Published
Title: CryoEM reveals the structure of an archaeal pilus involved in twitching motility
Authors: Isupov, M.N. / Gaines, M. / Daum, B. / Hanus, C.
History
DepositionDec 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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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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