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- EMDB-10890: cryo-electron density map of the P140-P110 heterodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-10890
Titlecryo-electron density map of the P140-P110 heterodimer
Map data
Sample
  • Complex: P140-P110 heterodimer
    • Protein or peptide: Mgp-operon protein 3
    • Protein or peptide: Adhesin P1
KeywordsP110/P140 Nap Mycoplasma genitalium surface adhesin / CELL ADHESION
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 G37 (bacteria) / Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsScheffer MP / Aparicio D
Funding support Germany, 2 items
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, 2020-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yrk
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10890.png

Downloads & links

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Map

FileDownload / File: emd_10890.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 270 pix.
= 283.5 Å		1.05 Å/pix.
x 270 pix.
= 283.5 Å		1.05 Å/pix.
x 270 pix.
= 283.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.012912566 - 0.033811565
Average (Standard dev.)0.00014913664 (±0.0014534903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 283.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z283.500283.500283.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.0130.0340.000

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Supplemental data

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Sample components

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Entire : P140-P110 heterodimer

EntireName: P140-P110 heterodimer
Components
  • Complex: P140-P110 heterodimer
    • Protein or peptide: Mgp-operon protein 3
    • Protein or peptide: Adhesin P1

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Supramolecule #1: P140-P110 heterodimer

SupramoleculeName: P140-P110 heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasma genitalium G37 (bacteria)

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Macromolecule #1: Mgp-operon protein 3

MacromoleculeName: Mgp-operon protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) (bacteria)
Molecular weightTheoretical: 84.816969 KDa
Recombinant expressionOrganism: Mycoplasma genitalium G37 (bacteria)
SequenceString: TFLVKEDSKN VTAYTPFATP ITDSKSDLVS LAQLDSSYQI ADQTIHNTNL FVLFKSRDVK VKYESSGSNN ISFDSTSQGE KPSYVVEFT NSTGIKWTMV KKYQLDVPNV SSDMNQVLKN LILEQPLTKY TLNSSLAKEK GKTQREVHLG SGQANQWTSQ R NQHDLNNN ...String:
TFLVKEDSKN VTAYTPFATP ITDSKSDLVS LAQLDSSYQI ADQTIHNTNL FVLFKSRDVK VKYESSGSNN ISFDSTSQGE KPSYVVEFT NSTGIKWTMV KKYQLDVPNV SSDMNQVLKN LILEQPLTKY TLNSSLAKEK GKTQREVHLG SGQANQWTSQ R NQHDLNNN PSPNASTGFK LTTGNAYRKL SESWPIYEPI DGTKQGKGKD SSGWSSTEEN EAKNDAPSVS SGTFNKYLNT KQ ALESIGI LFDDQTPRNV ITQLYYASTS KLAVTNNHIV VMGNSFLPSM WYWVVERSAQ ENASNKPTWF ANTNLDWGED KQK QFVENQ LGYKETTSTN SHNFHSKSFT QPAYLISGID SVNDQIIFSG FKAGSVGYDS SSSSSSSTKD QALAWSTTTS LDSK TGYKD LVTNDTGLNG PINGSFSIQD TFSFVVPYSG NHTNNGTTGP IKTAYPVKKD QKSTVKINSL INATPLNSYG DEGIG VFDA LGLNYNFKSN QERLPSRTDQ IFVYGIVSPN ELRSAKSSAD STGSDTKVNW SNTQSRYLPV PYNYSEGIID ADGFKR PEN RGASVTTFSG LKSIAPDGFA NSIANFSVGL KAGIDPNPVM SGKKANYGAV VLTRGGVVRL NFNPGNDSLL STTDNNI AP ISFSFTPFTA AESAVDLTTF KEVTYNQESG LWSYIFDSSL KPSHDGKQTP VTDNMGFSVI TVSRTGIELN QDQATTTL D VAPSALAVQS GIQSTTQTLT GVLPLSEEFS AVIAKDSDQN KIDIYKNNNG LFEIDT

UniProtKB: Mgp-operon protein 3

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Macromolecule #2: Adhesin P1

MacromoleculeName: Adhesin P1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) (bacteria)
Molecular weightTheoretical: 128.447648 KDa
Recombinant expressionOrganism: Mycoplasma genitalium G37 (bacteria)
SequenceString: QAVDETLTPW TWNNNNFSSL KITGENPGSF GLVRSQNDNL NISSVTKDNL KYLNAVEKYL DGQQNFAIRR YDNNGRALYD INLAKMENP STVQRGLNGE PIFDPFKGFG LTGNAPTDWN EIKGKVPVEV VQSPHSPNLY FVLLVPKVAL EYHNLNNQVV K ESLEVSSF ...String:
QAVDETLTPW TWNNNNFSSL KITGENPGSF GLVRSQNDNL NISSVTKDNL KYLNAVEKYL DGQQNFAIRR YDNNGRALYD INLAKMENP STVQRGLNGE PIFDPFKGFG LTGNAPTDWN EIKGKVPVEV VQSPHSPNLY FVLLVPKVAL EYHNLNNQVV K ESLEVSSF NPTQRLQKDS PVKDSSKQGE KLSETTASSM SSGMATSTRA KALKVEVERG SQSDSLLKND FAKKPLKHKN SS GEVKLEA EKEFTEAWKP LLTTDQIARE KGMGATVVSF YDAPYSENHT AFGLVDHIDP KKMVENYPPS WKTPKWNHHG IWD YNARNL LLQTTGFFNP RRHPEWFDEG QAKADNTSPG FKVGDTDHKK DGFKKNSSSP IALPFEAYFA NIGNMVAIGN SVFI FGGNG HATKMFTTNP LSIGVFRIKY TDNFSKSSVT GWPYAVLFGG LINPQTNGLK DLPLGTNRWF EYVPRMAVSG VKWVG NQLV LAGTLTMGDT ATVPRLKYDQ LEKHLNLVAQ GQGLLREDLQ IFTPYGWANR PDIPVGAWLQ DEMGSKFGPH YFLNNP DIQ DNVNNDTVEA LISSYKNTDK LKHVYPYRYS GLYAWQLFNW SNKLTNTPLS ANFVNENSYA PNSLFAAILN EDLLTGL SD KIFYGKENEF AENEADRFNQ LLSLNPNPNT NWARYLNVVQ RFTTGPNLDS STFDQFLDFL PWIGNGKPFS NSPSASTP L PTFSNINVGV KSMITQHLNK ENTRWVFIPN FSPDIWTGAG YRVQSANQKN GIPFEQVKPS NNSTPFDPNS DDNKVTPSG GSSKPTTYPA LPNSISPTSD WINALTFTNK NNPQRNQLLL RSLLGTIPVL INKSGDSNDQ FNKDSEQKWD KTETNEGNLP GFGEVNGLY NAALLHTYGF FGTNTNSTDP KIGFKADSSS SSSSTLVGSG LNWTSQDVGN LVVINDTSFG FQLGGWFITF T DFIRPRTG YLGITLSSLQ DQTIIWADQP WTSFKGSYLD SDGTPKSLWD PTALKSLPNN PTLSPSFQLY QPNKVKAYQT TN TYNKLIE PVDATSAATN MTSLLKLLTT KNIKAKLGKG TASNNGGGVS QTINTITTTG NISEGLKEET SIQAETLKKF FDS KQNNKS EIGIGDSTFT KMDGKLTGVV STPLVNLING QGAT

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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 7.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 6 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Details: Resolution is anisotropic / Number images used: 37009
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6rut

residue_range: 59-1243, source_name: PDB, initial_model_type: experimental model

6r3t

residue_range: 25-936, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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