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- PDB-7a02: Bacillus endospore appendages form a novel family of disulfide-li... -

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Basic information

Entry
Database: PDB / ID: 7a02
TitleBacillus endospore appendages form a novel family of disulfide-linked pili
ComponentsDUF3992 domain-containing protein
KeywordsUNKNOWN FUNCTION / Pilli / Endospore / Gram-Positive / Helical reconstruction / Disulphide bridge
Function / homologyEndospore appendages core / Endospore appendages / DUF3992 domain-containing protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsPradhan, B. / Liedtke, J. / Sleutel, M. / Lindback, T. / Llarena, A.K. / Brynildsrud, O. / Aspholm, M. / Remaut, H.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0818N Belgium
Citation
Journal: EMBO J / Year: 2021
Title: Endospore Appendages: a novel pilus superfamily from the endospores of pathogenic Bacilli.
Authors: Brajabandhu Pradhan / Janine Liedtke / Mike Sleutel / Toril Lindbäck / Ephrem Debebe Zegeye / Kristin O Sullivan / Ann-Katrin Llarena / Ola Brynildsrud / Marina Aspholm / Han Remaut /
Abstract: Bacillus cereus sensu lato is a group of Gram-positive endospore-forming bacteria with high ecological diversity. Their endospores are decorated with micrometer-long appendages of unknown identity ...Bacillus cereus sensu lato is a group of Gram-positive endospore-forming bacteria with high ecological diversity. Their endospores are decorated with micrometer-long appendages of unknown identity and function. Here, we isolate endospore appendages (Enas) from the food poisoning outbreak strain B. cereus NVH 0075-95 and find proteinaceous fibers of two main morphologies: S- and L-Ena. By using cryoEM and 3D helical reconstruction of S-Enas, we show these to represent a novel class of Gram-positive pili. S-Enas consist of single domain subunits with jellyroll topology that are laterally stacked by β-sheet augmentation. S-Enas are longitudinally stabilized by disulfide bonding through N-terminal connector peptides that bridge the helical turns. Together, this results in flexible pili that are highly resistant to heat, drought, and chemical damage. Phylogenomic analysis reveals a ubiquitous presence of the ena-gene cluster in the B. cereus group, which include species of clinical, environmental, and food importance. We propose Enas to represent a new class of pili specifically adapted to the harsh conditions encountered by bacterial spores.
#1: Journal: Biorxiv / Year: 2020
Title: Bacillus endospore appendages form a novel family of disulfide-linked pili
Authors: Pradhan, B. / Liedtke, J. / Sleutel, M. / Lindback, T. / Llarena, A.K. / Brynildsrud, O. / Aspholm, M. / Remaut, H.
History
DepositionAug 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_id_ISSN / _em_admin.last_update

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Assembly

Deposited unit
A: DUF3992 domain-containing protein
B: DUF3992 domain-containing protein
C: DUF3992 domain-containing protein
D: DUF3992 domain-containing protein
E: DUF3992 domain-containing protein
F: DUF3992 domain-containing protein
G: DUF3992 domain-containing protein
H: DUF3992 domain-containing protein
I: DUF3992 domain-containing protein
J: DUF3992 domain-containing protein
K: DUF3992 domain-containing protein
L: DUF3992 domain-containing protein
M: DUF3992 domain-containing protein
N: DUF3992 domain-containing protein
O: DUF3992 domain-containing protein
P: DUF3992 domain-containing protein
Q: DUF3992 domain-containing protein
R: DUF3992 domain-containing protein
S: DUF3992 domain-containing protein
T: DUF3992 domain-containing protein
U: DUF3992 domain-containing protein
V: DUF3992 domain-containing protein
W: DUF3992 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)279,74223
Polymers279,74223
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
DUF3992 domain-containing protein


Mass: 12162.675 Da / Num. of mol.: 23
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: B1995_14460, B2J90_04405, BACERE00183_02460, CNQ78_18995
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y6A695
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Ena1B / Type: ORGANELLE OR CELLULAR COMPONENT
Details: In vitro assembled Bacillus endospore appendage comprising the subunit Ena1B
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus cereus (bacteria) / Strain: NVH 0075-95 / Organelle: endospore appendage
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pET28a
Buffer solutionpH: 7
Buffer componentFormula: H2O
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298.15 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 60000 X / Calibrated defocus min: 500 nm / Calibrated defocus max: 3500 nm / Alignment procedure: BASIC
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER
Image recordingElectron dose: 64.66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3000

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2SerialEMimage acquisition
4CTFFIND4.2CTF correction
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 3.43721 ° / Axial rise/subunit: 32.3504 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 100495
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65466 / Symmetry type: HELICAL
Atomic model buildingB value: 27.4 / Protocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00818952
ELECTRON MICROSCOPYf_angle_d0.69425898
ELECTRON MICROSCOPYf_dihedral_angle_d17.2072737
ELECTRON MICROSCOPYf_chiral_restr0.0523335
ELECTRON MICROSCOPYf_plane_restr0.0023197

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