[English] 日本語
Yorodumi
- EMDB-20957: Anthrax toxin protective antigen channels bound to edema factor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20957
TitleAnthrax toxin protective antigen channels bound to edema factor
Map data
Sample
  • Complex: Anthrax toxin protective antigen channels bound to edema factor
    • Protein or peptide: Protective antigen
    • Protein or peptide: Calmodulin-sensitive adenylate cyclase
  • Ligand: CALCIUM IONCalcium
Keywordstranslocase / anthrax toxin / protective antigen / edema factor
Function / homology
Function and homology information


positive regulation of apoptotic process in another organism / calcium- and calmodulin-responsive adenylate cyclase activity / calmodulin dependent kinase signaling pathway / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / host cell cytosol / negative regulation of MAPK cascade / small molecule binding / Uptake and function of anthrax toxins ...positive regulation of apoptotic process in another organism / calcium- and calmodulin-responsive adenylate cyclase activity / calmodulin dependent kinase signaling pathway / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / host cell cytosol / negative regulation of MAPK cascade / small molecule binding / Uptake and function of anthrax toxins / catalytic complex / host cell endosome membrane / protein homooligomerization / metallopeptidase activity / toxin activity / calmodulin binding / host cell plasma membrane / extracellular region / ATP binding / membrane / identical protein binding / metal ion binding
Similarity search - Function
: / Oedema factor (EF), alpha-helical domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Anthrax toxin, lethal/endema factor ...: / Oedema factor (EF), alpha-helical domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
Protective antigen / Calmodulin-sensitive adenylate cyclase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHardenbrook NJ / Liu S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R01GM071940/AI094386/DE025567 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R21AI124020 United States
CitationJournal: Nat Commun / Year: 2020
Title: Atomic structures of anthrax toxin protective antigen channels bound to partially unfolded lethal and edema factors.
Authors: Nathan J Hardenbrook / Shiheng Liu / Kang Zhou / Koyel Ghosal / Z Hong Zhou / Bryan A Krantz /
Abstract: Following assembly, the anthrax protective antigen (PA) forms an oligomeric translocon that unfolds and translocates either its lethal factor (LF) or edema factor (EF) into the host cell. Here, we ...Following assembly, the anthrax protective antigen (PA) forms an oligomeric translocon that unfolds and translocates either its lethal factor (LF) or edema factor (EF) into the host cell. Here, we report the cryo-EM structures of heptameric PA channels with partially unfolded LF and EF at 4.6 and 3.1-Å resolution, respectively. The first α helix and β strand of LF and EF unfold and dock into a deep amphipathic cleft, called the α clamp, which resides at the interface of two PA monomers. The α-clamp-helix interactions exhibit structural plasticity when comparing the structures of lethal and edema toxins. EF undergoes a largescale conformational rearrangement when forming the complex with the channel. A critical loop in the PA binding interface is displaced for about 4 Å, leading to the weakening of the binding interface prior to translocation. These structures provide key insights into the molecular mechanisms of translocation-coupled protein unfolding and translocation.
History
DepositionNov 14, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseMar 4, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6uzd
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20957.png

Downloads & links

-
Map

FileDownload / File: emd_20957.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.08165202 - 0.20097578
Average (Standard dev.)0.000361506 (±0.006953357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z321.000321.000321.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0820.2010.000

-
Supplemental data

-
Sample components

-
Entire : Anthrax toxin protective antigen channels bound to edema factor

EntireName: Anthrax toxin protective antigen channels bound to edema factor
Components
  • Complex: Anthrax toxin protective antigen channels bound to edema factor
    • Protein or peptide: Protective antigen
    • Protein or peptide: Calmodulin-sensitive adenylate cyclase
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: Anthrax toxin protective antigen channels bound to edema factor

SupramoleculeName: Anthrax toxin protective antigen channels bound to edema factor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 613 kDa/nm

-
Macromolecule #1: Protective antigen

MacromoleculeName: Protective antigen / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 82.768828 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: EVKQENRLLN ESESSSQGLL GYYFSDLNFQ APMVVTSSTT GDLSIPSSEL ENIPSENQYF QSAIWSGFIK VKKSDEYTFA TSADNHVTM WVDDQEVINK ASNSNKIRLE KGRLYQIKIQ YQRENPTEKG LDFKLYWTDS QNKKEVISSD NLQLPELKQK S SNSRKKRS ...String:
EVKQENRLLN ESESSSQGLL GYYFSDLNFQ APMVVTSSTT GDLSIPSSEL ENIPSENQYF QSAIWSGFIK VKKSDEYTFA TSADNHVTM WVDDQEVINK ASNSNKIRLE KGRLYQIKIQ YQRENPTEKG LDFKLYWTDS QNKKEVISSD NLQLPELKQK S SNSRKKRS TSAGPTVPDR DNDGIPDSLE VEGYTVDVKN KRTFLSPWIS NIHEKKGLTK YKSSPEKWST ASDPYSDFEK VT GRIDKNV SPEARHPLVA AYPIVHVDME NIILSKNEDQ STQNTDSQTR TISKNTSTSR THTSEVHGNA EVHASFFDIG GSV SAGFSN SNSSTVAIDH SLSLAGERTW AETMGLNTAD TARLNANIRY VNTGTAPIYN VLPTTSLVLG KNQTLATIKA KENQ LSQIL APNNYYPSKN LAPIALNAQD DFSSTPITMN YNQFLELEKT KQLRLDTDQV YGNIATYNFE NGRVRVDTGS NWSEV LPQI QETTARIIFN GKDLNLVERR IAAVNPSDPL ETTKPDMTLK EALKIAFGFN EPNGNLQYQG KDITEFDFNF DQQTSQ NIK NQLAELNATN IYTVLDKIKL NAKMNILIRD KRFHYDRNNI AVGADESVVK EAHREVINSS TEGLLLNIDK DIRKILS GY IVEIEDTEGL KEVINDRYDM LNISSLRQDG KTFIDFKKYN DKLPLYISNP NYKVNVYAVT KENTIINPSE NGDTSTNG I KKILIFSKKG YEIG

UniProtKB: Protective antigen

-
Macromolecule #2: Calmodulin-sensitive adenylate cyclase

MacromoleculeName: Calmodulin-sensitive adenylate cyclase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: adenylate cyclase
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 88.955578 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MNEHYTESDI KRNHKTEKNK TEKEKFKDSI NNLVKTEFTN ETLDKIQQTQ DLLKKIPKDV LEIYSELGGE IYFTDIDLVE HKELQDLSE EEKNSMNSRG EKVPFASRFV FEKKRETPKL IINIKDYAIN SEQSKEVYYE IGKGISLDII SKDKSLDPEF L NLIKSLSD ...String:
MNEHYTESDI KRNHKTEKNK TEKEKFKDSI NNLVKTEFTN ETLDKIQQTQ DLLKKIPKDV LEIYSELGGE IYFTDIDLVE HKELQDLSE EEKNSMNSRG EKVPFASRFV FEKKRETPKL IINIKDYAIN SEQSKEVYYE IGKGISLDII SKDKSLDPEF L NLIKSLSD DSDSSDLLFS QKFKEKLELN NKSIDINFIK ENLTEFQHAF SLAFSYYFAP DHRTVLELYA PDMFEYMNKL EK GGFEKIS ESLKKEGVEK DRIDVLKGEK ALKASGLVPE HADAFKKIAR ELNTYILFRP VNKLATNLIK SGVATKGLNV HGK SSDWGP VAGYIPFDQD LSKKHGQQLA VEKGNLENKK SITEHEGEIG KIPLKLDHLR IEELKENGII LKGKKEIDNG KKYY LLESN NQVYEFRISD ENNEVQYKTK EGKITVLGEK FNWRNIEVMA KNVEGVLKPL TADYDLFALA PSLTEIKKQI PQKEW DKVV NTPNSLEKQK GVTNLLIKYG IERKPDSTKG TLSNWQKQML DRLNEAVKYT GYTGGDVVNH GTEQDNEEFP EKDNEI FII NPEGEFILTK NWEMTGRFIE KNITGKDYLY YFNRSYNKIA PGNKAYIEWT DPITKAKINT IPTSAEFIKN LSSIRRS SN VGVYKDSGDK DEFAKKESVK KIAGYLSDYY NSANHIFSQE KKRKISIFRG IQAYNEIENV LKSKQIAPEY KNYFQYLK E RITNQVQLLL THQKSNIEFK LLYKQLNFTE NETDNFEVFQ KIIDEK

UniProtKB: Calmodulin-sensitive adenylate cyclase

-
Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 62.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6224

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 72864

+
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