[English] 日本語
Yorodumi
- EMDB-22194: PmtCD in peptidisc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22194
TitlePmtCD in peptidisc
Map data
Sample
  • Complex: PmtCD
    • Protein or peptide: PmtC
    • Protein or peptide: PmtD
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsZeytuni N / Hu J / Worrall LJ / Strynadka NCJ
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)Operating grant Canada
CitationJournal: Sci Adv / Year: 2020
Title: Structural insight into the ATP-driven exporter of virulent peptide toxins.
Authors: N Zeytuni / S W Dickey / J Hu / H T Chou / L J Worrall / J A N Alexander / M L Carlson / M Nosella / F Duong / Z Yu / M Otto / N C J Strynadka /
Abstract: is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs ... is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membrane-destructive cytolytic peptides that are exported to the host-cell environment by a designated adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, the PSM transporter (PmtABCD). Here, we demonstrate that the minimal Pmt unit necessary for PSM export is PmtCD and provide its first atomic characterization by single-particle cryo-EM and x-ray crystallography. We have captured the transporter in the ATP-bound state at near atomic resolution, revealing a type II ABC exporter fold, with an additional cytosolic domain. Comparison to a lower-resolution nucleotide-free map displaying an "open" conformation and putative hydrophobic inner chamber of a size able to accommodate the binding of two PSM peptides provides mechanistic insight and sets the foundation for therapeutic design.
History
DepositionJun 21, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0355
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0355
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22194.png

Downloads & links

-
Map

FileDownload / File: emd_22194.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 150 pix.
= 196.5 Å		1.31 Å/pix.
x 150 pix.
= 196.5 Å		1.31 Å/pix.
x 150 pix.
= 196.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0355 / Movie #1: 0.0355
Minimum - Maximum-0.16970164 - 0.23830341
Average (Standard dev.)0.0007075577 (±0.007834807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 196.49998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z196.500196.500196.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.1700.2380.001

-
Supplemental data

-
Sample components

-
Entire : PmtCD

EntireName: PmtCD
Components
  • Complex: PmtCD
    • Protein or peptide: PmtC
    • Protein or peptide: PmtD

-
Supramolecule #1: PmtCD

SupramoleculeName: PmtCD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: PmtCD ABC exporter
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightExperimental: 120 KDa

-
Macromolecule #1: PmtC

MacromoleculeName: PmtC / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MKLEHITKKY GSNVVLNDID FDFGDSRIVG LIGKNGVGKT TVMKVMNGNI IKFDGKVDID NADNIGFLIE HPKLYDNKSG LYNLKLFAQV LGKGFDKAYT DKIIDAFGMR PYIKKKVKKY SMGMKQKLAI AVSLMNKPKF LILDEPTNGM DPDGSIDVLT TIKSLVNELD ...String:
MKLEHITKKY GSNVVLNDID FDFGDSRIVG LIGKNGVGKT TVMKVMNGNI IKFDGKVDID NADNIGFLIE HPKLYDNKSG LYNLKLFAQV LGKGFDKAYT DKIIDAFGMR PYIKKKVKKY SMGMKQKLAI AVSLMNKPKF LILDEPTNGM DPDGSIDVLT TIKSLVNELD MRILISSHKL EDIELICDRA VFLRDGHFVQ DVNMEEGVAS DTTIVTVDHK DFDRTEKYLA EHFQLQNVDK ADGHLMINAQ KNYQVILKAL SELDIYPKYI ETRKSSLRDT YFNINQRGDK

-
Macromolecule #2: PmtD

MacromoleculeName: PmtD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: MHHHHHHHHH HSSGLVPRGS HRILNLVKYD LYSIFKSPLT YLAILVVSSL IATQSILMAN SMDNPKHIIV YGSVFAAAKW LLLIIGLMFV VKTITRDFSQ GTIQLYMSKV KTRVGYIISK TISIILISIL FALIHYVILI VVQASSNGKN LAFSKYVDNL WFFLIFLLFF ...String:
MHHHHHHHHH HSSGLVPRGS HRILNLVKYD LYSIFKSPLT YLAILVVSSL IATQSILMAN SMDNPKHIIV YGSVFAAAKW LLLIIGLMFV VKTITRDFSQ GTIQLYMSKV KTRVGYIISK TISIILISIL FALIHYVILI VVQASSNGKN LAFSKYVDNL WFFLIFLLFF GLFLFLITLA SQKTAMIFSL GVFLVLIVPF IKPFITFIPR YGEKVLDAFD YIPFAYLTDK MISSNFDFSN WQWVISLGSI VIFFILNILY VAKKDI

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClsodium chloride

Details: Solution made fresh from concentrated stocks and filtered
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1132044
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 113197
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

+
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