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- EMDB-36428: Fibril form of serine peptidase Vpr -

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Basic information

Entry
Database: EMDB / ID: EMD-36428
TitleFibril form of serine peptidase Vpr
Map data
Sample
  • Cell: Bacillus amyloliquefaciens
    • Protein or peptide: S8 family serine peptidase
KeywordsSerine peptidase / fibril / PROTEIN 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)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsCao Q / Cheng Y
Funding support China, 1 items
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, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36428.png

Downloads & links

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Map

FileDownload / File: emd_36428.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 2.4
Minimum - Maximum-4.358324 - 15.580684
Average (Standard dev.)0.000000000004157 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36428_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36428_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus amyloliquefaciens

EntireName: Bacillus amyloliquefaciens (bacteria)
Components
  • Cell: Bacillus amyloliquefaciens
    • Protein or peptide: S8 family serine peptidase

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Supramolecule #1: Bacillus amyloliquefaciens

SupramoleculeName: Bacillus amyloliquefaciens / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus amyloliquefaciens (bacteria)

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Macromolecule #1: S8 family serine peptidase

MacromoleculeName: S8 family serine peptidase / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Bacillus amyloliquefaciens (bacteria)
Molecular weightTheoretical: 85.965602 KDa
SequenceString: LKKGIIRYLL PAFVLSFTLS TSSQAAPASK PQTPDLEKAE VFGDIDMTTG KQTTVIVELK EKSLAEAKEL GKAQTKSKLK SERSKVKKK ALKTIKHGKI NREYEQVFSG FSMKLPANEI PKLLSDQDVK AVYPNVTYHT DQLKDKDITL SKDAVSPQMD D SAPYIGAN ...String:
LKKGIIRYLL PAFVLSFTLS TSSQAAPASK PQTPDLEKAE VFGDIDMTTG KQTTVIVELK EKSLAEAKEL GKAQTKSKLK SERSKVKKK ALKTIKHGKI NREYEQVFSG FSMKLPANEI PKLLSDQDVK AVYPNVTYHT DQLKDKDITL SKDAVSPQMD D SAPYIGAN DAWKLGYTGK GVKVAIIDTG VEYKHPDLKK NFGQYKGYDF VDNDYDPEET PSGDPRGAST DHGTHVAGTV AA NGTIKGV APDATLLAYR VLGPGGSGTT ENVIAGIERA VQDGADVMNL SLGNSVNNPD WATSTALDWA MSEGVTAVTS NGN SGPNNW TVGSPGTSRE AISVGATQLP LNEYAVSFGS YSSAKVMGYN KEDDIKALNK KETELIEAGI GEQKDFEGKD LKGK VAVVK RGSIAFVDKA DNAKKAGAIG MVVYNNAPGE IEANVPGMSV PTVKLSSEDG EKLVSQLKAG GTKATFHLSV AKSLT EQMA DFSSRGPVMD TWMIKPDVSA PGVNIVSTIP THDPADPYGY GSKQGTSMAS PHVAGAAAVI KQAKPKWSPE QIKAAL MNT AETLTDADGD VYPHNAQGAG SIRIMKAIKA DSLVAPGSYS YGTFMKDKGN ETKKETFTIE NQSSIRKSYQ LEYSFNG TG ITVSGTDRVV IPAHQTGKVN AKVKVNAKKV KAGTYEGTVT VREGGKTVAK VPTLLIVKEP DYPRVTSIDV QDGTTQGT Y QIETYLPAGA EELAFLVYDS NLDFVGQAGI YKKQDKGYQY FDWNGKVNGD TALPAGEYYM LAYAANKGKS SQVLTEKPF IIE

UniProtKB: S8 family serine peptidase

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.6000000000000005 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 20.46 Å
Applied symmetry - Helical parameters - Δ&Phi: -68.75 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76671
FSC plot (resolution estimation)

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