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- PDB-6yrk: P140-P110 complex fitted into the cryo-electron density map of th... -

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Basic information

Entry
Database: PDB / ID: 6yrk
TitleP140-P110 complex fitted into the cryo-electron density map of the heterodimer
Components
  • Adhesin P1
  • Mgp-operon protein 3
KeywordsCELL 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
Adhesin P1, C-terminal domain / Adhesin P1, N-terminal / Adhesin P1 / Mycoplasma adhesin P1, C-terminal / Mycoplasma adhesin P1, N-terminal / MgpC adhesin / Mgp-operon protein 3, C-terminal domain / MgpC adhesin / MGP3 C-terminal domain
Similarity search - Domain/homology
Adhesin P1 / Mgp-operon protein 3
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsScheffer, M.P. / Aparicio, D.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR1653/6-1 Germany
German Research Foundation (DFG)SFB902 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
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-10890
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Mgp-operon protein 3
B: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)213,2652
Polymers213,2652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5510 Å2
ΔGint-20 kcal/mol
Surface area64340 Å2
MethodPISA

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Components

#1: Protein Mgp-operon protein 3 / Mgp3 / ORF-3 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
#2: Protein Adhesin P1 / Attachment protein / Cytadhesin P1 / MgPa


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: P140-P110 heterodimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycoplasma genitalium G37 (bacteria)
Source (recombinant)Organism: Mycoplasma genitalium G37 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 7.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 0.92/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
4RELION3CTF correction
7UCSF Chimera1.13.1model fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 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 buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-IDPdb chain residue range
16RUT

6rut

6RUT159-1243
26R3T

6r3t

6R3T225-936

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