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- EMDB-17592: Sub-tomogram average of the open conformation of the Nap adhesion... -

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Basic information

Entry
Database: EMDB / ID: EMD-17592
TitleSub-tomogram average of the open conformation of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.
Map data
Sample
  • Cell: Mildly lysed M. genitalium cells
    • Protein or peptide: Mgp-operon protein 3
    • Protein or peptide: Adhesin P1
  • Ligand: POTASSIUM ION
  • Ligand: PHOSPHATE ION
  • Ligand: water
KeywordsAdhesion / Mycoplasma genitalium / 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 speciesMycoplasmoides genitalium G37 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 17.0 Å
AuthorsSprankel L / Scheffer MP / Frangakis AF
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: PLoS Pathog / Year: 2023
Title: Cryo-electron tomography reveals the binding and release states of the major adhesion complex from Mycoplasma genitalium.
Authors: Lasse Sprankel / Margot P Scheffer / Sina Manger / Utz H Ermel / Achilleas S Frangakis /
Abstract: The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host ...The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host cell. The nap particle is composed of two P140-P110 heterodimers, the structure of which was recently solved. However, the interpretation of the mechanism by which the mycoplasma cells orchestrate adhesion remained challenging. Here, we provide cryo-electron tomography structures at ~11 Å resolution, which allow for the distinction between the bound and released state of the nap particle, displaying the in vivo conformational states. Fitting of the atomically resolved structures reveals that bound sialylated oligosaccharides are stabilized by both P110 and P140. Movement of the stalk domains allows for the transfer of conformational changes from the interior of the cell to the binding pocket, thus having the capability of an active release process. It is likely that the same mechanism can be transferred to other Mycoplasma species that belong to the pneumoniae cluster.
History
DepositionJun 9, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17592.png

Downloads & links

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Map

FileDownload / File: emd_17592.map.gz / Format: CCP4 / Size: 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.)
5.2 Å/pix.
x 64 pix.
= 332.8 Å		5.2 Å/pix.
x 64 pix.
= 332.8 Å		5.2 Å/pix.
x 64 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000229
Minimum - Maximum-0.0006011666 - 0.000952682
Average (Standard dev.)0.00000514689 (±0.00009559006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17592_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17592_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17592_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mildly lysed M. genitalium cells

EntireName: Mildly lysed M. genitalium cells
Components
  • Cell: Mildly lysed M. genitalium cells
    • Protein or peptide: Mgp-operon protein 3
    • Protein or peptide: Adhesin P1
  • Ligand: POTASSIUM ION
  • Ligand: PHOSPHATE ION
  • Ligand: water

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Supramolecule #1: Mildly lysed M. genitalium cells

SupramoleculeName: Mildly lysed M. genitalium cells / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycoplasmoides 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: Mycoplasmoides genitalium G37 (bacteria)
Molecular weightTheoretical: 114.553211 KDa
SequenceString: MKTMRKQIYK KAYWLLLPFL PLALANTFLV KEDSKNVTAY TPFATPITDS KSDLVSLAQL DSSYQIADQT IHNTNLFVLF KSRDVKVKY ESSGSNNISF DSTSQGEKPS YVVEFTNSTN IGIKWTMVKK YQLDVPNVSS DMNQVLKNLI LEQPLTKYTL N SSLAKEKG ...String:
MKTMRKQIYK KAYWLLLPFL PLALANTFLV KEDSKNVTAY TPFATPITDS KSDLVSLAQL DSSYQIADQT IHNTNLFVLF KSRDVKVKY ESSGSNNISF DSTSQGEKPS YVVEFTNSTN IGIKWTMVKK YQLDVPNVSS DMNQVLKNLI LEQPLTKYTL N SSLAKEKG KTQREVHLGS GQANQWTSQR NQHDLNNNPS PNASTGFKLT TGNAYRKLSE SWPIYEPIDG TKQGKGKDSS GW SSTEENE AKNDAPSVSG GGSSSGTFNK YLNTKQALES IGILFDDQTP RNVITQLYYA STSKLAVTNN HIVVMGNSFL PSM WYWVVE RSAQENASNK PTWFANTNLD WGEDKQKQFV ENQLGYKETT STNSHNFHSK SFTQPAYLIS GIDSVNDQII FSGF KAGSV GYDSSSSSSS SSSSSTKDQA LAWSTTTSLD SKTGYKDLVT NDTGLNGPIN GSFSIQDTFS FVVPYSGNHT NNGTT GPIK TAYPVKKDQK STVKINSLIN ATPLNSYGDE GIGVFDALGL NYNFKSNQER LPSRTDQIFV YGIVSPNELR SAKSSA DST GSDTKVNWSN TQSRYLPVPY NYSEGIIDAD GFKRPENRGA SVTTFSGLKS IAPDGFANSI ANFSVGLKAG IDPNPVM SG KKANYGAVVL TRGGVVRLNF NPGNDSLLST TDNNIAPISF SFTPFTAAES AVDLTTFKEV TYNQESGLWS YIFDSSLK P SHDGKQTPVT DNMGFSVITV SRTGIELNQD QATTTLDVAP SALAVQSGIQ STTQTLTGVL PLSEEFSAVI AKDSDQNKI DIYKNNNGLF EIDTQLSNSV ATNNGGLAPS YTENRVDAWG KVEFADNSVL QARNLVDKTV DEIINTPEIL NSFFRFTPAF EDQKATLVA TKQSDTSLSV SPRIQFLDGN FYDLNSTIAG VPLNIGFPSR VFAGFAALPA WVIPVSVGSS VGILFILLVL G LGIGIPMY RVRKLQDASF VNVFKKVDTL TTAVGSVYKK IITQTGVVKK APSALKAANP SVKKPAAFLK PPVQPPSKPE GE QKAVEVK SEETKS

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: Mycoplasmoides genitalium G37 (bacteria)
Molecular weightTheoretical: 159.809297 KDa
SequenceString: MHQPKKRLAK KSWAFLTAAL TLGVITGVGG YFLFNQNKQR SSVSNFAYQP KQLSVKHQQA VDETLTPWTW NNNNFSSLKI TGENPGSFG LVRSQNDNLN ISSVTKNSSD DNLKYLNAVE KYLDGQQNFA IRRYDNNGRA LYDINLAKME NPSTVQRGLN G EPIFDPFK ...String:
MHQPKKRLAK KSWAFLTAAL TLGVITGVGG YFLFNQNKQR SSVSNFAYQP KQLSVKHQQA VDETLTPWTW NNNNFSSLKI TGENPGSFG LVRSQNDNLN ISSVTKNSSD DNLKYLNAVE KYLDGQQNFA IRRYDNNGRA LYDINLAKME NPSTVQRGLN G EPIFDPFK GFGLTGNAPT DWNEIKGKVP VEVVQSPHSP NLYFVLLVPK VALEYHNLNN QVVKESLEVK ATQSSFNPTQ RL QKDSPVK DSSKQGEKLS ETTASSMSSG MATSTRAKAL KVEVERGSQS DSLLKNDFAK KPLKHKNSSG EVKLEAEKEF TEA WKPLLT TDQIAREKGM GATVVSFYDA PYSENHTAFG LVDHIDPKKM VENYPPSWKT PKWNHHGIWD YNARNLLLQT TGFF NPRRH PEWFDEGQAK ADNTSPGFKV GDTDHKKDGF KKNSSSPIAL PFEAYFANIG NMVAIGNSVF IFGGNGHATK MFTTN PLSI GVFRIKYTDN FSKSSVTGWP YAVLFGGLIN PQTNGLKDLP LGTNRWFEYV PRMAVSGVKW VGNQLVLAGT LTMGDT ATV PRLKYDQLEK HLNLVAQGQG LLREDLQIFT PYGWANRPDI PVGAWLQDEM GSKFGPHYFL NNPDIQDNVN NDTVEAL IS SYKNTDKLKH VYPYRYSGLY AWQLFNWSNK LTNTPLSANF VNENSYAPNS LFAAILNEDL LTGLSDKIFY GKENEFAE N EADRFNQLLS LNPNPNTNWA RYLNVVQRFT TGPNLDSSTF DQFLDFLPWI GNGKPFSNSP SPSTSASSST PLPTFSNIN VGVKSMITQH LNKENTRWVF IPNFSPDIWT GAGYRVQSAN QKNGIPFEQV KPSNNSTPFD PNSDDNKVTP SGGSSKPTTY PALPNSISP TSDWINALTF TNKNNPQRNQ LLLRSLLGTI PVLINKSGDS NDQFNKDSEQ KWDKTETNEG NLPGFGEVNG L YNAALLHT YGFFGTNTNS TDPKIGFKAD SSSSSSSTLV GSGLNWTSQD VGNLVVINDT SFGFQLGGWF ITFTDFIRPR TG YLGITLS SLQDQTIIWA DQPWTSFKGS YLDSDGTPKS LWDPTALKSL PNSSTTYDTN PTLSPSFQLY QPNKVKAYQT TNT YNKLIE PVDATSAATN MTSLLKLLTT KNIKAKLGKG TASSQGNNNG GGVSQTINTI TTTGNISEGL KEETSIQAET LKKF FDSKQ NNKSEIGIGD STFTKMDGKL TGVVSTPLVN LINGQGATSD SDTEKISFKP GNQIDFNRLF TLPVTELFDP NTMFV YDQY VPLLVNLPSG FDQASIRLKV ISYSVENQTL GVRLEFKDPQ TQQFIPVLNA SSTGPQTVFQ PFNQWADYVL PLIVTV PIV VIILSVTLGL TIGIPMHRNK KALQAGFDLS NKKVDVLTKA VGSVFKEIIN RTGISNAPKK LKQATPTKPT PKTPPKP PV KQ

UniProtKB: Adhesin P1

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 99 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsMildy lysed M. genitalium cells

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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: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 9689
ExtractionNumber tomograms: 420 / Number images used: 36720
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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