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- PDB-8jmw: Fibril form of serine peptidase Vpr -

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Basic information

Entry
Database: PDB / ID: 8jmw
TitleFibril form of serine peptidase Vpr
ComponentsS8 family serine peptidase
KeywordsPROTEIN FIBRIL / Serine peptidase / fibril
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Vpr-like peptidase, catalytic domain / FlgD Ig-like domain / FlgD Ig-like domain / PA domain superfamily / PA domain / PA domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site ...Vpr-like peptidase, catalytic domain / FlgD Ig-like domain / FlgD Ig-like domain / PA domain superfamily / PA domain / PA domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
S8 family serine peptidase
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsCao, Q. / Cheng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271276 China
CitationJournal: Nat Commun / Year: 2023
Title: Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM.
Authors: Yijia Cheng / Jianting Han / Meinai Song / Shuqin Zhang / Qin Cao /
Abstract: Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab- ...Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab-cultured Bacillus amyloiquefaciens and discover an unreported fibril species in addition to the flagellar fibrils. These previously unknown fibrils are composed of Vpr, an extracellular serine peptidase. We find that Vpr assembles into fibrils in an enzymatically active form, potentially representing a strategy of enriching Vpr activities around bacterial cells. Vpr fibrils are also observed under other culture conditions and around other Bacillus bacteria, such as Bacillus subtilis, which may suggest a general mechanism across all Bacillus bacterial groups. Taken together, our study reveals fibrils outside the bacterial cell and sheds light on the physiological role of these extracellular fibrils.
History
DepositionJun 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S8 family serine peptidase
B: S8 family serine peptidase
C: S8 family serine peptidase
D: S8 family serine peptidase
E: S8 family serine peptidase
F: S8 family serine peptidase
G: S8 family serine peptidase
H: S8 family serine peptidase
I: S8 family serine peptidase
J: S8 family serine peptidase
K: S8 family serine peptidase
L: S8 family serine peptidase
M: S8 family serine peptidase
N: S8 family serine peptidase
O: S8 family serine peptidase
P: S8 family serine peptidase
Q: S8 family serine peptidase
R: S8 family serine peptidase


Theoretical massNumber of molelcules
Total (without water)1,547,38118
Polymers1,547,38118
Non-polymers00
Water0
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
S8 family serine peptidase


Mass: 85965.602 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Bacillus amyloliquefaciens (bacteria) / References: UniProt: A0A6A8LCF5

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Bacillus amyloliquefaciens / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus amyloliquefaciens (bacteria)
Buffer solutionpH: 7.4
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: 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 FIELDBright-field microscopy / Nominal defocus max: 4600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -68.75 ° / Axial rise/subunit: 20.46 Å / Axial symmetry: C2
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76671 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00771046
ELECTRON MICROSCOPYf_angle_d0.6196660
ELECTRON MICROSCOPYf_dihedral_angle_d4.7469900
ELECTRON MICROSCOPYf_chiral_restr0.04710746
ELECTRON MICROSCOPYf_plane_restr0.00512672

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