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- EMDB-55147: Cryo-EM density map of essential Mycoplasma pneumoniae lipoprotei... -

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Basic information

Entry
Database: EMDB / ID: EMD-55147
TitleCryo-EM density map of essential Mycoplasma pneumoniae lipoprotein Mpn444 at 3.74 A
Map data
Sample
  • Complex: Essential Mycoplasma pneumoniae lipoprotein Mpn444
    • Protein or peptide: Uncharacterized lipoprotein MG309 homolog
KeywordsPPIase Chaperone Mycoplasma pneumoniae lipoprotein / CHAPERONE
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: 3.74 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: Structures of the essential Mycoplasma pneumoniae lipoproteins Mpn444 and Mpn436 reveal a peptidyl-prolyl isomerase domain involved in extracellular protein folding
Authors: Manger S / Keles I / Frangakis AS / Scheffer MP / Mantanya MS
History
DepositionSep 25, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55147.png

Downloads & links

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Map

FileDownload / File: emd_55147.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: 0.216
Minimum - Maximum-1.4437735 - 2.3684204
Average (Standard dev.)-0.0003562684 (±0.024061492)
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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Half map: #1

Fileemd_55147_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_55147_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
Details: Recombinantly expressed in E.coli without the N-terminal signal peptide
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 145 KDa

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Macromolecule #1: Uncharacterized lipoprotein MG309 homolog

MacromoleculeName: Uncharacterized lipoprotein MG309 homolog / type: protein_or_peptide / ID: 1
Details: Full-length protein without N-terminal signal peptide
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 146.441781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHTFTRKVKW PFMFTAIGLT FGIVAVACAQ PTASTVEGLF KPSSAFADRT DFSLSSILQK SLINRESFNQ YLAMRLAPVL RTFYEDNYD TDIKERLNGF TADTDNAFVS QEQNLRNQFR ENYLVHLQTD IFDNTGGNQA AWKLRDVNNK IIDDFISRIF A KNFVEYVQ ...String:
MHTFTRKVKW PFMFTAIGLT FGIVAVACAQ PTASTVEGLF KPSSAFADRT DFSLSSILQK SLINRESFNQ YLAMRLAPVL RTFYEDNYD TDIKERLNGF TADTDNAFVS QEQNLRNQFR ENYLVHLQTD IFDNTGGNQA AWKLRDVNNK IIDDFISRIF A KNFVEYVQ DGVGPLTKPT KSLIENTSNF KNIKLQPKFV NKNAKLKINN DAVYAAIQDK LLDQFITNEN PNLVSRVVFT NE TPVDGFD NYFNTKVIQS PTPSYQFQVF NKYNQQSGGT KGANGFNLLA SNLKSYKNDQ SKGIDIPNKF SSDSGGKLLL KAS DMFDTF DPSFSAAFIQ GYLALQKKSK GADSKEVDSL IKDKSIIENF FVDNNTQAAA AARAASSSSE GTIQLKTASD GGGT TQSTV HKTDLVKIFG DKDVFAGEYK QQIGNTNANQ TGGGGSGGGG GTSTGSSTGS STETTTGNSS KAVVDLIEVK KDSSS QPDY ILSRGKDGIH LMAVDGGSHY LTESGRDVAK QKKFLLFRAL QTKYGLVDTD TTYDFKLFDE VKKYFDTNRI LFLFEA LLD LSSDTNNKDN FLSYPQFKKF ADSIKSIEKD LKELVQAHYK QAVFNETAVA ENKVTLKLAE RNQPFIDNER NNQIEQN GL AAKLPYEQDA KTGHYNDLGN YYKDIIDNVD KKGTSTVKTT SSNTGQTKNF SEEVVSKLKD NKKKVEEAAK KHVEALKV F TIPSPLYSQV ILVQTKLSFT PESTSLGLNL ALNNYLTSTE LQNSIKLSYF QEDEAFKKII DITNLTFSQQ SGGTGGTNG NNNLTADNWK IFKETYLLDL FESQAQKSIF GHVGSSDKNS STKTGIEGVL DTLYSSLNLE ERLDSDDVID YLSYLYTAHW LLKDNLKNY KQSLQSKLSR TSNAFLVWSV DSEKNKNDSQ STLSSTASST SNTGLIQLRS VVSLAQNQAA GQGGDNNSDI T QTEVKNPN FVFGSSVYDW TNSKTPEVNR AADDTSSFFY TKSSSSSTGA AQSSATVLRS LNQASGMTTK TAKNRYGFRG IV TSSTSGS LPEAVSRRLF KQFVNQTEKG VKVGGQMLIT TAKSGKATLV LKQQADDAES TTNNAYKGAL FSFGSMDNLK NII NGIQTQ TEFDALYNHL TSDLNIDVTG VDKNKTLTEQ KTSLTSFVDS NFKQSTQSAQ RGDTSARSAR SATVQIKKTQ EDNQ NTNYK DVFSRFDGYI GDNKVEEKNY TSYQFLSDGG KYHATFVKQV NLDDVEKIGT DSLKQEDSSK DKRLNLSLEE FLAAI ALEA LDPNNQTQAI NALISGNKKG LVKVGDFRIF SSISAQWVRR F

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 pH 7.4, 200 mM NaCl and 0 to 0.01% LMNG or 1 mM CHAPSO
GridModel: C-flat-1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
Details: Nominal blot force -3 Wait time 10 s Blotting time 14 s Before freezing, Whatman 595 filter papers were incubated for 1 h in the Vitrobot chamber at 100% relative humidity and 278K..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.5 sec. / 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: 3.6 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

DetailsThe camera was operated in dose-fractionation counting mode with a dose rate of ~16 electrons per A2 per s, resulting in a total dose of 50 electrons per A2. The frame time was adjusted to 1 frame per 1 electron per A2
Particle selectionNumber selected: 6832694
CTF correctionSoftware - Name: cryoSPARC (ver. v4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Number images used: 432841
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.3)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. v4.5.3)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9srq:
Full-length cryo-EM structure of essential Mycoplasma pneumoniae lipoprotein Mpn444

PDB-9srs:
Partial cryo-EM structure of essential Mycoplasma pneumoniae lipoprotein Mpn444 (flexible loops excluded)

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