[English] 日本語
Yorodumi
- EMDB-10259: Sub-tomogram average of the Nap adhesion complex from the human p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10259
TitleSub-tomogram average of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.
Map dataSub-tomogram average of the surface adhesin (NAP) complex from Mycoplasma genitalium cells by cryo-electron tomography.
Sample
  • Complex: Sub-tomogram average of the Nap adhesin from Mycoplasma genitalium cells.
Biological speciesMycoplasma genitalium G37 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsScheffer MP / Aparicio D
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research FoundationFR1653/6-1 Germany
German Research FoundationSFB902 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Structure and mechanism of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.
Authors: David Aparicio / Margot P Scheffer / Marina Marcos-Silva / David Vizarraga / Lasse Sprankel / Mercè Ratera / Miriam S Weber / Anja Seybert / Sergi Torres-Puig / Luis Gonzalez-Gonzalez / ...Authors: David Aparicio / Margot P Scheffer / Marina Marcos-Silva / David Vizarraga / Lasse Sprankel / Mercè Ratera / Miriam S Weber / Anja Seybert / Sergi Torres-Puig / Luis Gonzalez-Gonzalez / Julian Reitz / Enrique Querol / Jaume Piñol / Oscar Q Pich / Ignacio Fita / Achilleas S Frangakis /
Abstract: Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane ...Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane adhesion complex called Nap comprising proteins P110 and P140. Here we report the crystal structure of P140 both alone and in complex with the N-terminal domain of P110. By cryo-electron microscopy (cryo-EM) and tomography (cryo-ET) we find closed and open Nap conformations, determined at 9.8 and 15 Å, respectively. Both crystal structures and the cryo-EM structure are found in a closed conformation, where the sialic acid binding site in P110 is occluded. By contrast, the cryo-ET structure shows an open conformation, where the binding site is accessible. Structural information, in combination with functional studies, suggests a mechanism for attachment and release of M. genitalium to and from the host cell receptor, in which Nap conformations alternate to sustain motility and guarantee infectivity.
History
DepositionAug 26, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseJun 24, 2020-
UpdateJun 24, 2020-
Current statusJun 24, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0117
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0117
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10259.png

Downloads & links

-
Map

FileDownload / File: emd_10259.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of the surface adhesin (NAP) complex from Mycoplasma genitalium cells by cryo-electron tomography.
Voxel sizeX=Y=Z: 2.2 Å
Density
Contour LevelBy AUTHOR: 0.0117 / Movie #1: 0.0117
Minimum - Maximum0 - 0.022023555
Average (Standard dev.)0.010204303 (±0.0008645539)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean0.0000.0220.010

-
Supplemental data

-
Sample components

-
Entire : Sub-tomogram average of the Nap adhesin from Mycoplasma genitaliu...

EntireName: Sub-tomogram average of the Nap adhesin from Mycoplasma genitalium cells.
Components
  • Complex: Sub-tomogram average of the Nap adhesin from Mycoplasma genitalium cells.

-
Supramolecule #1: Sub-tomogram average of the Nap adhesin from Mycoplasma genitaliu...

SupramoleculeName: Sub-tomogram average of the Nap adhesin from Mycoplasma genitalium cells.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasma genitalium G37 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE
DetailsMildly detergent-lysed cells

-
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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 54 / Number images used: 11000
CTF correctionSoftware - Name: Super-sampling SART (ver. 2)
Software - details: Kunz, M. & Frangakis, A. S. Three-dimensional CTF correction improves the resolution of electron tomograms. Journal of structural biology 197, 114-122, doi: 10.1016
Details: Tomograms were reconstructed by super-sampling SART with 3D contrast transfer function (CTF) correction.
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 8800

-
Atomic model buiding 1

Initial model(PDB ID:

6r41

,

6rut

)
RefinementProtocol: RIGID BODY FIT

+
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