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- EMDB-30233: Cryo-EM structure of the human pathogen Mycoplasma pneumoniae P1 -

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Basic information

Entry
Database: EMDB / ID: EMD-30233
TitleCryo-EM structure of the human pathogen Mycoplasma pneumoniae P1
Map data
Sample
  • Organelle or cellular component: Nap protein P1
    • Protein or peptide: Adhesin P1
KeywordsSialic acid receptor / STRUCTURAL PROTEIN
Function / homology
Function and homology information


attachment organelle / adhesion of symbiont to microvasculature / cell projection / cell surface / membrane / 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
Similarity search - Domain/homology
Biological speciesMycoplasma pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKawamoto A / Kenri T
Funding support Japan, 7 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25000013 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Japan Society for the Promotion of Science (JSPS)24117002 Japan
Japan Society for the Promotion of Science (JSPS)24390107 Japan
Japan Society for the Promotion of Science (JSPS)17H01544 Japan
Japan Society for the Promotion of Science (JSPS)JPMJCR19S5 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Immunodominant proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae.
Authors: David Vizarraga / Akihiro Kawamoto / U Matsumoto / Ramiro Illanes / Rosa Pérez-Luque / Jesús Martín / Rocco Mazzolini / Paula Bierge / Oscar Q Pich / Mateu Espasa / Isabel Sanfeliu / ...Authors: David Vizarraga / Akihiro Kawamoto / U Matsumoto / Ramiro Illanes / Rosa Pérez-Luque / Jesús Martín / Rocco Mazzolini / Paula Bierge / Oscar Q Pich / Mateu Espasa / Isabel Sanfeliu / Juliana Esperalba / Miguel Fernández-Huerta / Margot P Scheffer / Jaume Pinyol / Achilleas S Frangakis / Maria Lluch-Senar / Shigetarou Mori / Keigo Shibayama / Tsuyoshi Kenri / Takayuki Kato / Keiichi Namba / Ignacio Fita / Makoto Miyata / David Aparicio /
Abstract: Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which ...Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which form a transmembrane adhesion complex. Here we report the structure of P1, determined by X-ray crystallography and cryo-electron microscopy, and the X-ray structure of P40/P90. Contrary to what had been suggested, the binding site for sialic acid was found in P40/P90 and not in P1. Genetic and clinical variability concentrates on the N-terminal domain surfaces of P1 and P40/P90. Polyclonal antibodies generated against the mostly conserved C-terminal domain of P1 inhibited adhesion of M. pneumoniae, and serology assays with sera from infected patients were positive when tested against this C-terminal domain. P40/P90 also showed strong reactivity against human infected sera. The architectural elements determined for P1 and P40/P90 open new possibilities in vaccine development against M. pneumoniae infections.
History
DepositionApr 15, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0512
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0512
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bwm
  • Surface level: 0.0512
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30233.png

Downloads & links

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Map

FileDownload / File: emd_30233.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.69 Å
Density
Contour LevelBy AUTHOR: 0.0512 / Movie #1: 0.0512
Minimum - Maximum-0.18383971 - 0.33919975
Average (Standard dev.)0.00053704745 (±0.009749232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 193.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.690.690.69
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z193.200193.200193.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1840.3390.001

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Supplemental data

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Sample components

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Entire : Nap protein P1

EntireName: Nap protein P1
Components
  • Organelle or cellular component: Nap protein P1
    • Protein or peptide: Adhesin P1

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Supramolecule #1: Nap protein P1

SupramoleculeName: Nap protein P1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria)
Molecular weightTheoretical: 170 kDa/nm

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Macromolecule #1: Adhesin P1

MacromoleculeName: Adhesin P1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: M129
Molecular weightTheoretical: 143.778484 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: NAINPRLTPW TYRNTSFSSL PLTGENPGAW ALVRDNSAKG ITAGSGSQQT TYDPTRTEAA LTASTTFALR RYDLAGRALY DLDFSKLNP QTPTRDQTGQ ITFNPFGGFG LSGAAPQQWN EVKNKVPVEV AQDPSNPYRF AVLLVPRSVV YYEQLQRGLG L PQQRTESG ...String:
NAINPRLTPW TYRNTSFSSL PLTGENPGAW ALVRDNSAKG ITAGSGSQQT TYDPTRTEAA LTASTTFALR RYDLAGRALY DLDFSKLNP QTPTRDQTGQ ITFNPFGGFG LSGAAPQQWN EVKNKVPVEV AQDPSNPYRF AVLLVPRSVV YYEQLQRGLG L PQQRTESG QNTSTTGAMF GLKVKNAEAD TAKSNEKLQG AEATGSSTTS GSGQSTQRGG SSGDTKVKAL KIEVKKKSDS ED NGQLQLE KNDLANAPIK RSEESGQSVQ LKADDFGTAL SSSGSGGNSN PGSPTPWRPW LATEQIHKDL PKWSASILIL YDA PYARNR TAIDRVDHLD PKAMTANYPP SWRTPKWNHH GLWDWKARDV LLQTTGFFNP RRHPEWFDGG QTVADNEKTG FDVD NSENT KQGFQKEADS DKSAPIALPF EAYFANIGNL TWFGQALLVF GGNGHVTKSA HTAPLSIGVF RVRYNATGTS ATVTG WPYA LLFSGMVNKQ TDGLKDLPFN NNRWFEYVPR MAVAGAKFVG RELVLAGTIT MGDTATVPRL LYDELESNLN LVAQGQ GLL REDLQLFTPY GWANRPDLPI GAWSSSSSSS HNAPYYFHNN PDWQDRPIQN VVDAFIKPWE DKNGKDDAKY IYPYRYS GM WAWQVYNWSN KLTDQPLSAD FVNENAYQPN SLFAAILNPE LLAALPDKVK YGKENEFAAN EYERFNQKLT VAPTQGTN W SHFSPTLSRF STGFNLVGSV LDQVLDYVPW IGNGYRYGNN HRGVDDITAP QTSAGSSSGI STNTSGSRSF LPTFSNIGV GLKANVQATL GGSQTMITGG SPRRTLDQAN LQLWTGAGWR NDKASSGQSD ENHTKFTSAT GMDQQGQSGT SAGNPDSLKQ DNISKSGDS LTTQDGNAID QQEATNYTNL PPNLTPTADW PNALSFTNKN NAQRAQLFLR GLLGSIPVLV NRSGSDSNKF Q ATDQKWSY TDLHSDQTKL NLPAYGEVNG LLNPALVETY FGNTRAGGSG SNTTSSPGIG FKIPEQNNDS KATLITPGLA WT PQDVGNL VVSGTTVSFQ LGGWLVTFTD FVKPRAGYLG LQLTGLDASD ATQRALIWAP RPWAAFRGSW VNRLGRVESV WDL KGVWAD QAQSDSQGST TTATRNALPE HPNALAFQVS VVEASAYKPN TSSGQTQSTN SSPYLHLVKP KKVTQSDKLD DDLK NLLDP NQVRTKLRQS FGTDHSTQPQ PQSLKTTTPV FGTSSGNLSS VLSGGGAGGG SSGSGQSGVD LSPVEKVSGW LVGQL PSTS DGNTSSTNNL APNTNTGNDV VGVGRLSESN AAKMNDDVDG IVRT

UniProtKB: Adhesin P1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.75 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 96000
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 78.9 K / Max: 78.9 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 5279 / Average exposure time: 36.33 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 68014

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Atomic model buiding 1

Initial modelPDB ID:

6rc9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7bwm:
Cryo-EM structure of the human pathogen Mycoplasma pneumoniae P1

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