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- PDB-8w20: Umb1 umbrella toxin particle -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8w20
TitleUmb1 umbrella toxin particle
Components
  • Intein C-terminal splicing domain-containing protein
  • Secreted esterase
  • Secreted proteinSecretory protein
KeywordsTOXIN / Streptomyces / Umbrella toxin particles / Alanine leucine phenylalanine-rich (ALF) repeat proteins / Seattle structural genomics center for infectious disease / SSGCID
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Protein of unknown function DUF312, ALF / Short repeats of unknown function / Pretoxin HINT domain / Double-stranded DNA deaminase toxin A / Double-stranded DNA deaminase toxin A / FG-GAP-like repeat / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region ...Protein of unknown function DUF312, ALF / Short repeats of unknown function / Pretoxin HINT domain / Double-stranded DNA deaminase toxin A / Double-stranded DNA deaminase toxin A / FG-GAP-like repeat / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / FG-GAP repeat / Integrin alpha, N-terminal / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Intein C-terminal splicing domain-containing protein / Secreted protein / Secreted esterase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsPark, Y.J. / Zhao, Q. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio, F. / Mougous, J.D. / Veesler, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: Nature / Year: 2024
Title: Streptomyces umbrella toxin particles block hyphal growth of competing species
Authors: Park, Y.J. / Veesler, D. / Mougous, J.D.
History
DepositionFeb 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Secreted protein
C: Secreted esterase
A: Intein C-terminal splicing domain-containing protein
D: Secreted protein
E: Secreted esterase
F: Secreted protein
G: Secreted esterase
H: Secreted protein
I: Secreted esterase
J: Secreted protein
K: Secreted esterase


Theoretical massNumber of molelcules
Total (without water)500,83411
Polymers500,83411
Non-polymers00
Water0
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
Secreted protein / Secretory protein


Mass: 17186.270 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9ACV3
#2: Protein
Secreted esterase


Mass: 54437.102 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: endogenous tags to purified the complex from natural source
Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9ACV4
#3: Protein Intein C-terminal splicing domain-containing protein


Mass: 142716.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: endogenous tags to purified the complex from natural source
Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9ACV2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Umb1 umbrella toxin particle / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Buffer solutionpH: 8
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: 3000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386275 / Symmetry type: POINT

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