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Yorodumi- PDB-6rut: Mycoplasma Genitalium Heterodimer Nap Complex (P140-P110 globular) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rut | ||||||
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Title | Mycoplasma Genitalium Heterodimer Nap Complex (P140-P110 globular) | ||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / Adhesion complex | ||||||
Function / homology | Function and homology information adhesion of symbiont to microvasculature / cell adhesion / plasma membrane Similarity search - Function | ||||||
Biological species | Mycoplasma genitalium G37 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Fita, I. / Aparicio, D. | ||||||
Funding support | Spain, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rut.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6rut.ent.gz | 2.5 MB | Display | PDB format |
PDBx/mmJSON format | 6rut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rut_validation.pdf.gz | 529.1 KB | Display | wwPDB validaton report |
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Full document | 6rut_full_validation.pdf.gz | 676.2 KB | Display | |
Data in XML | 6rut_validation.xml.gz | 267.5 KB | Display | |
Data in CIF | 6rut_validation.cif.gz | 363.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/6rut ftp://data.pdbj.org/pub/pdb/validation_reports/ru/6rut | HTTPS FTP |
-Related structure data
Related structure data | 6s3uC 6yrkC 6r3tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 87378.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: MG192 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22747 #2: Protein | Mass: 147979.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: mgpA, MG191 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P20796 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 23% PEG MME 4% PGA 0.1M Sodium cacodylate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97897 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97897 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→157.28 Å / Num. obs: 189359 / % possible obs: 73.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 47.32 Å2 / CC1/2: 0.873 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.65→2.7 Å / Num. unique obs: 784 / CC1/2: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R3T Resolution: 2.65→121.66 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.851 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.366
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Displacement parameters | Biso mean: 40.36 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→121.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.78 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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