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- EMDB-51459: CryoEM structure of essential Mycoplasma pneumoniae lipoprotein Mpn444 -

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Basic information

Entry
Database: EMDB / ID: EMD-51459
TitleCryoEM structure of essential Mycoplasma pneumoniae lipoprotein Mpn444
Map data
Sample
  • Complex: Essential Mycoplasma pneumoniae lipoprotein Mpn444
    • Protein or peptide: Uncharacterized lipoprotein MG309 homolog
KeywordsSurface Protein Lipoprotein Mycoplasma pneumoniae / UNKNOWN FUNCTION
Function / homologyProtein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / Uncharacterized lipoprotein MG309 homolog
Function and homology information
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsManger S / Keles I
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: To Be Published
Title: Structural characterization of an essential lipoprotein of Mycoplasma pneumoniae
Authors: Keles I / Manger S / Frangakis AS
History
DepositionAug 30, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51459.png

Downloads & links

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Map

FileDownload / File: emd_51459.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 480 pix.
= 441.6 Å		0.92 Å/pix.
x 480 pix.
= 441.6 Å		0.92 Å/pix.
x 480 pix.
= 441.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-1.3111373 - 2.0781004
Average (Standard dev.)-0.00019171697 (±0.019796656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 441.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51459_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51459_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_51459_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 : Essential Mycoplasma pneumoniae lipoprotein Mpn444

EntireName: Essential Mycoplasma pneumoniae lipoprotein Mpn444
Components
  • Complex: Essential Mycoplasma pneumoniae lipoprotein Mpn444
    • Protein or peptide: Uncharacterized lipoprotein MG309 homolog

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Supramolecule #1: Essential Mycoplasma pneumoniae lipoprotein Mpn444

SupramoleculeName: Essential Mycoplasma pneumoniae lipoprotein Mpn444 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Macromolecule #1: Uncharacterized lipoprotein MG309 homolog

MacromoleculeName: Uncharacterized lipoprotein MG309 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 144.800641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MCAQPTASTV EGLFKPSSAF ADRTDFSLSS ILQKSLINRE SFNQYLAMRL APVLRTFYED NYDTDIKERL NGFTADTDNA FVSQEQNLR NQFRENYLVH LQTDIFDNTG GNQAAWKLRD VNNKIIDDFI SRIFAKNFVE YVQDGVGPLT KPTKSLIENT S NFKNIKLQ ...String:
MCAQPTASTV EGLFKPSSAF ADRTDFSLSS ILQKSLINRE SFNQYLAMRL APVLRTFYED NYDTDIKERL NGFTADTDNA FVSQEQNLR NQFRENYLVH LQTDIFDNTG GNQAAWKLRD VNNKIIDDFI SRIFAKNFVE YVQDGVGPLT KPTKSLIENT S NFKNIKLQ PKFVNKNAKL KINNDAVYAA IQDKLLDQFI TNENPNLVSR VVFTNETPVD GFDNYFNTKV IQSPTPSYQF QV FNKYNQQ SGGTKGANGF NLLASNLKSY KNDQSKGIDI PNKFSSDSGG KLLLKASDMF DTFDPSFSAA FIQGYLALQK KSK GADSKE VDSLIKDKSI IENFFVDNNT QAAAAARAAS SSSEGTIQLK TASDGGGTTQ STVHKTDLVK IFGDKDVFAG EYKQ QIGNT NANQTGGGGS GGGGGTSTGS STGSSTETTT GNSSKAVVDL IEVKKDSSSQ PDYILSRGKD GIHLMAVDGG SHYLT ESGR DVAKQKKFLL FRALQTKYGL VDTDTTYDFK LFDEVKKYFD TNRILFLFEA LLDLSSDTNN KDNFLSYPQF KKFADS IKS IEKDLKELVQ AHYKQAVFNE TAVAENKVTL KLAERNQPFI DNERNNQIEQ NGLAAKLPYE QDAKTGHYND LGNYYKD II DNVDKKGTST VKTTSSNTGQ TKNFSEEVVS KLKDNKKKVE EAAKKHVEAL KVFTIPSPLY SQVILVQTKL SFTPESTS L GLNLALNNYL TSTELQNSIK LSYFQEDEAF KKIIDITNLT FSQQSGGTGG TNGNNNLTAD NWKIFKETYL LDLFESQAQ KSIFGHVGSS DKNSSTKTGI EGVLDTLYSS LNLEERLDSD DVIDYLSYLY TAHWLLKDNL KNYKQSLQSK LSRTSNAFLV WSVDSEKNK NDSQSTLSST ASSTSNTGLI QLRSVVSLAQ NQAAGQGGDN NSDITQTEVK NPNFVFGSSV YDWTNSKTPE V NRAADDTS SFFYTKSSSS STGAAQSSAT VLRSLNQASG MTTKTAKNRY GFRGIVTSST SGSLPEAVSR RLFKQFVNQT EK GVKVGGQ MLITTAKSGK ATLVLKQQAD DAESTTNNAY KGALFSFGSM DNLKNIINGI QTQTEFDALY NHLTSDLNID VTG VDKNKT LTEQKTSLTS FVDSNFKQST QSAQRGDTSA RSARSATVQI KKTQEDNQNT NYKDVFSRFD GYIGDNKVEE KNYT SYQFL SDGGKYHATF VKQVNLDDVE KIGTDSLKQE DSSKDKRLNL SLEEFLAAIA LEALDPNNQT QAINALISGN KKGLV KVGD FRIFSSISAQ WVRRFAAALE HHHHHH

UniProtKB: Uncharacterized lipoprotein MG309 homolog

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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

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris 200 mM NaCl 0-0.01% LMNG or 1mM CHAPSO
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 7811 / Average electron dose: 50.0 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: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5832694
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3.) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3.) / Number images used: 156400
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3.)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3.)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.5.3.)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9gn0:
CryoEM structure of essential Mycoplasma pneumoniae lipoprotein Mpn444

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