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- EMDB-43737: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF... -

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Basic information

Entry
Database: EMDB / ID: EMD-43737
TitleUmb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)
Map data
Sample
  • Complex: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)
    • Protein or peptide: Intein C-terminal splicing domain-containing protein
    • Protein or peptide: Secreted proteinSecretory protein
    • Protein or peptide: Secreted esterase
KeywordsStreptomyces / Umbrella toxin particles / Alanine leucine phenylalanine-rich (ALF) repeat proteins / Seattle structural genomics center for infectious disease / SSGCID / TOXIN
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(2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsPark YJ / Zhao Q / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio F / Mougous JD / Veesler D
Funding support United States, 1 items
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 YJ / Veesler D / Mougous JD
History
DepositionFeb 19, 2024-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43737.png

Downloads & links

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Map

FileDownload / File: emd_43737.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 304 pix.
= 512.544 Å		1.69 Å/pix.
x 304 pix.
= 512.544 Å		1.69 Å/pix.
x 304 pix.
= 512.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.686 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-6.5915785 - 9.149419
Average (Standard dev.)0.00026179783 (±0.071626596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 512.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_43737_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43737_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_43737_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 : Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF...

EntireName: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)
Components
  • Complex: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)
    • Protein or peptide: Intein C-terminal splicing domain-containing protein
    • Protein or peptide: Secreted proteinSecretory protein
    • Protein or peptide: Secreted esterase

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Supramolecule #1: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF...

SupramoleculeName: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)

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Macromolecule #1: Intein C-terminal splicing domain-containing protein

MacromoleculeName: Intein C-terminal splicing domain-containing protein / type: protein_or_peptide / ID: 1
Details: endogenous tags to purified the complex from natural source
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 142.716734 KDa
SequenceString: MRRRIPSRTP GSGAKQKSWF PRRSLQVLLS AGMLSGLLGT PAALAAEPAP LPANVRADIV GYWETGGAGL KAAAEQALLG GDEAIRKFL ADAPSIQHDD NRIDAARMAM TGGSGLRQAA KDAIRLSPAE LEKFLLYGYE EPLDDDHKVE IARLINLGGP G VREAGKAA ...String:
MRRRIPSRTP GSGAKQKSWF PRRSLQVLLS AGMLSGLLGT PAALAAEPAP LPANVRADIV GYWETGGAGL KAAAEQALLG GDEAIRKFL ADAPSIQHDD NRIDAARMAM TGGSGLRQAA KDAIRLSPAE LEKFLLYGYE EPLDDDHKVE IARLINLGGP G VREAGKAA LQGTAEEREL FLNSGQYTAQ QDDNRVDVAR LATTGGPNVQ AAAKVALRGT PEDMVEFLEV GQFTARNRDQ EH ATIAELI KQAELAGKQA DDARKTAEES SKKAVDASQL AKEAAQKAAE ETEAAKDDSQ KAAVKAKQAA DAARAAADAA QEA IGSANA ANRAARRAAL AAAQTASAAT AAAEAANKAY KAAIAAAGDE GKADEAKEAA KQARAAADAA TKSGLAAENA GLAS AAAAT ASTAAKSASS NARAAAGAAE EANQHADAAG VHSNEAALAA AEARRHADAA DRAADRSSAL AQRAATAAYG ARDAA NSAA EHANKAADYA DESAAHAGDS AAYAATAKRN AQAAQEAAKT ATAAVTKANE IFKLARETET ANLETRTDAA IERARS MKS ASETSITASA TTQVEALALN DTATELAKEA SRPDIDVQAT AAKGRQLAMQ AMKLLGPWHQ EAAARALSGT DQDVLDY LR TRWKEANHND IRQQIVDLST QSPYASVRTA AAEALNGTPE QIEAFHTTGQ YTAGSDDMKV DVARLANTGG PGVSQAAK T ALADGTGKTL ATFLQIGQYG ERLSDEKVVT ARLAETGSPE VQAAAKIALA GPPELLHEFV TTGQYMAKRK DDLADVHVN QVERLLAEGS LIAAEANEDA WRATEAAATA EGAAADAATA AEKAEASAAQ AKQHAADADA SADAATRSAA DAAASAATAR DAADRAAQD ATAAENSAAE AAFSAAYARD SASKADDAAD RARASALAAG KSADEAEAEA KEAWKTTRAL AEKEAEEARR K AAEERKRQ QEQAGEPKRV CIPHPTRETM IPIMPCAASP DDSMIMPGPV DPTIRAVVWE LAGLNDIKAC IDKPLSGNCV MA VVGVTPW GKFKLVSKLG NGLDAVKDAR GARRTVACLT GAAHSFPAGT RVLMADGTRR SIEQIEAGDL VTATDPTTGE TGA RTVTRT IHTPDDRNFT DVALADGSTL TSTTHHPYWS QNDQTWKNAG DLEAGDTLRT PQNTAVVIAA THDWPGLQDA YDLT VDGFH SYYVSTGTTD VLVHNNDNPC PDWVSKAWKK LPKRKSGDPT SGYVFEADGT LVWDSVLTSG RSPLSEDISA FLKGS PDFP NFPGYADVAH HAEAKIAWEM RTKMGKGKKL HIVINTNYVC PKVSSPNSMG CKQAVPAILY EDQTLYVHYP GASDAL ELK GTAKR

UniProtKB: Intein C-terminal splicing domain-containing protein

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Macromolecule #2: Secreted protein

MacromoleculeName: Secreted protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 17.18627 KDa
SequenceString:
MANTSRTRQA LMAIAVSVLA AGVTTLGVAH ADNGDAVAAA AEMPQAVEDF SYPGAAKIQA ETGAILKRGN GHMLMTSCDG SEDIQVMSR TGQKDFCFNV MAKPAYLTLE VPQAYGIWTS ADPVKTTIKD TDGTATVINA PANDFTGYGE AGSTGEPTTL I ELRVAG

UniProtKB: Secreted protein

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Macromolecule #3: Secreted esterase

MacromoleculeName: Secreted esterase / type: protein_or_peptide / ID: 3
Details: endogenous tags to purified the complex from natural source
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 54.437102 KDa
SequenceString: MFRMPRPIRA TALSAAVLAG ALASTPAQAT VGDPTTDAKL DFTARLTIGT DYRSCSGALV DTQWVLTAAS CFADDPNQPD TVAAGKPAQ LTRATVGRAD SNIANGYVRE VVELVPHPER DMVLARLDKA IPDIAPVRLA SDAPTAGTPL TAVGFGRTKD E WVPIQRHQ ...String:
MFRMPRPIRA TALSAAVLAG ALASTPAQAT VGDPTTDAKL DFTARLTIGT DYRSCSGALV DTQWVLTAAS CFADDPNQPD TVAAGKPAQ LTRATVGRAD SNIANGYVRE VVELVPHPER DMVLARLDKA IPDIAPVRLA SDAPTAGTPL TAVGFGRTKD E WVPIQRHQ GAFTVTSVTA GAVNVTGQGG DAICAGDTGG PLLQDKNGTL HLVGVNNRSM QGGCYGSETT STDAIAAMSD AD FVTQTVN RDLGTGNLSD LVASADFNSD GRTDVAAVLE DGSLHAFYAK PDGTLEYGRE LWNDNTWSPM VQIIGGDFNS DGN GDIAAV RSDGTLNLYT GTATGILNKS KPMWHDTSWK TIKQVTRFKF NGRDGLVAQW GDGNLYGYYT GTDGTLTGTK VKMW PDATW GKTRLTGTAD INADGRDDLT AVRDDGSLNW YAGNTKGGLD AARKLWPDNT WTPMKRIIGG DFNGDNKGDI AAVGG QSTL LLYTGTGTGT LNKGIAMRPA SGSHHHHHHH H

UniProtKB: Secreted esterase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
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: 3.0 µm / Nominal defocus min: 0.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 386275

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