[English] 日本語
Yorodumi
- EMDB-43737: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF... -

+
Open data


ID or keywords:

Loading...

-
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 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 ...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: Qinqin Zhao / Savannah Bertolli / Young-Jun Park / Yongjun Tan / Kevin J Cutler / Pooja Srinivas / Kyle L Asfahl / Citlali Fonesca-García / Larry A Gallagher / Yaqiao Li / Yaxi Wang / Devin ...Authors: Qinqin Zhao / Savannah Bertolli / Young-Jun Park / Yongjun Tan / Kevin J Cutler / Pooja Srinivas / Kyle L Asfahl / Citlali Fonesca-García / Larry A Gallagher / Yaqiao Li / Yaxi Wang / Devin Coleman-Derr / Frank DiMaio / Dapeng Zhang / S Brook Peterson / David Veesler / Joseph D Mougous /
Abstract: Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive. The production of these antibacterial molecules reflects the relentless ...Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles. Streptomyces coelicolor encodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of select Streptomyces species from among a diverse collection of bacteria screened. For one target, Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show that Streptomyces umbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly. Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.
History
DepositionFeb 19, 2024-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43737.png

Downloads & links

-
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 °

-
Supplemental data

-
Additional map: #1

Fileemd_43737_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43737_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43737_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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 protein
    • Protein or peptide: Secreted esterase

-
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)

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more