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Yorodumi- PDB-6yrk: P140-P110 complex fitted into the cryo-electron density map of th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yrk | |||||||||
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Title | P140-P110 complex fitted into the cryo-electron density map of the heterodimer | |||||||||
Components |
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Keywords | CELL ADHESION / P110/P140 Nap Mycoplasma genitalium surface adhesin | |||||||||
Function / homology | Function and homology information adhesion of symbiont to microvasculature / cell adhesion / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycoplasma genitalium (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Scheffer, M.P. / Aparicio, D. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6yrk.cif.gz | 727.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yrk.ent.gz | 593.2 KB | Display | PDB format |
PDBx/mmJSON format | 6yrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yrk_validation.pdf.gz | 768 KB | Display | wwPDB validaton report |
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Full document | 6yrk_full_validation.pdf.gz | 799.2 KB | Display | |
Data in XML | 6yrk_validation.xml.gz | 58.7 KB | Display | |
Data in CIF | 6yrk_validation.cif.gz | 89.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/6yrk ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yrk | HTTPS FTP |
-Related structure data
Related structure data | 10890MC 6rutC 6s3uC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 84816.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) (bacteria) Gene: MG192 / Production host: Mycoplasma genitalium G37 (bacteria) / References: UniProt: P22747 |
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#2: Protein | Mass: 128447.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) (bacteria) Gene: mgpA, MG191 / Production host: Mycoplasma genitalium G37 (bacteria) / References: UniProt: P20796 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: P140-P110 heterodimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Mycoplasma genitalium G37 (bacteria) |
Source (recombinant) | Organism: Mycoplasma genitalium G37 (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 7.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 0.92/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37009 / Details: Resolution is anisotropic / Num. of class averages: 6 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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