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- EMDB-55148: Cryo-EM density map of essential Mycoplasma pneumoniae lipoprotei... -

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Basic information

Entry
Database: EMDB / ID: EMD-55148
TitleCryo-EM density map of essential Mycoplasma pneumoniae lipoprotein Mpn436 at 3.65 A
Map data
Sample
  • Complex: Essential Mycoplasma pneumoniae lipoprotein Mpn436
    • Protein or peptide: Uncharacterized lipoprotein MG307 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 MG307 homolog
Function and homology information
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 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_55148.png

Downloads & links

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Map

FileDownload / File: emd_55148.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: 0.334
Minimum - Maximum-1.7794003 - 4.207458
Average (Standard dev.)0.0069382982 (±0.028917164)
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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Sample components

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Entire : Essential Mycoplasma pneumoniae lipoprotein Mpn436

EntireName: Essential Mycoplasma pneumoniae lipoprotein Mpn436
Components
  • Complex: Essential Mycoplasma pneumoniae lipoprotein Mpn436
    • Protein or peptide: Uncharacterized lipoprotein MG307 homolog

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Supramolecule #1: Essential Mycoplasma pneumoniae lipoprotein Mpn436

SupramoleculeName: Essential Mycoplasma pneumoniae lipoprotein Mpn436 / 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 MG307 homolog

MacromoleculeName: Uncharacterized lipoprotein MG307 homolog / type: protein_or_peptide / ID: 1
Details: Full-length protein without the N-terminal signal peptide
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 139.269438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKFLRKPQF WLLTLGGFLS TSVILAACAT PSNSALQTVF KARSSQFFNG EQGSLQSALT TALKNPVANK QFIAAPLLKA LEAWYENNE DKKITQFLKD TKSNVDSQYT TAVDKVVSAS RNKSLFVQQD LLDNAGGSEA TWKAQKLLEQ LISDFASRVF Q KNYLNYKK ...String:
MKKFLRKPQF WLLTLGGFLS TSVILAACAT PSNSALQTVF KARSSQFFNG EQGSLQSALT TALKNPVANK QFIAAPLLKA LEAWYENNE DKKITQFLKD TKSNVDSQYT TAVDKVVSAS RNKSLFVQQD LLDNAGGSEA TWKAQKLLEQ LISDFASRVF Q KNYLNYKK DGQVSTGPFT YDELHKEESW KNFEFSAPRF SETNDDFFAK IQSQVFDQWV EYTDPTLISQ VNYKYSAPSQ GL GQIYNRE KLKDKLTPSY AFPFFAEEKD IAPNQNVGNK RWKQLVKGEG AITDNNIGQS GTNSQKTGLL KYRNESNKGD FLD FPLNLS DTNETKQLVD ASNIVDQLEA ANLGAALNLK LQVFEQDNDE LPQIKELKED LNNTIVVDKS KDVEKASKTN ALFY NDQEG KQQQSDSDPI AGALDDIFAQ NTSEGTNLSK LAEQVKKAAA TKMEAKTAVL RTNNSKGQQN NYVVLDAAIP TFNST TSKS KNNSASNEVL VALKSGSINL RQVQQTDQNS YSPIKFRIVR NSTGVTVFGL DGGSYYLKQD STNKKSVSKQ SLTLLT KSS SGNSNKVLRD LDKQKQFLKF RAFQAKTNTF YSTNFAFSFP LNETLKSWFD KHRELILANA LVNASLDQKD KASKALT EA FNPYKELIKE FAPVALATTM ISFYFDQMKA LNNKLLERAR NLNQNVNQAN PTPWLNGLSA KLPYVNTNGN YEKLNNYF T FLITKTLWPK VGQEETSISE ESNKLKTKTA DVDKIRDKIL ENIQTKVNDF VKNKLKPALA PRPAYSNVIL LNVNNDKVL SSGANWSLAS LLQSDKVNPL SFMLLKQAFD NNDLFKKAQK LFKDIQEKSS NNGGMQSSST TNSDADALSK VIGNYYYTTW AKLTDKSIY GNPKDNKFDE LFKLAFEASI DEKSFNVDYK AVIDHYRFIY TLQWLVDQKL KNFKSLLKTN LKFGEVAFIA Y KNTETTNF SNPQGVFGSY FNYENSASEV KESTQTLDPN NFFYKTTTKP TVQAIQQVAS LALVQKQQMQ QNSTDHYGFT GL STSTSSM FDASSRDAIL QQITKTSLQQ YGSKDQLKKI IQGTNNQLLL DRIAVQLSGL NPSTTNGGSG KTIATYFQVD AVG NPTLDF QAKRKLLLDL LDQYQNYFGN GAQKSQRDST PSGTGNYLTY QNGSDKYTYT QFTYQDIDSL SLTTTSGTNN KIAS DVVAA LLLFQAADKG TQQLALSAIN KPQLNIGDKR IESGLKLLK

UniProtKB: Uncharacterized lipoprotein MG307 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

Concentration0.8 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 8 to 14 s. Before freezing, Whatman 595 filter papers were incubated for 1 h in the Vitrobot chamber at 100% relative humidity and 278K..
DetailsConcentration range from 0.5 mg/ml to 0.8 mg/ml

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Details: The camera was operated in dose-fractionation counting mode with a dose rate of ~16 electrons per A2 s-1, resulting in a total dose of 50 electrons per A2. The frame time was adjusted to 1 ...Details: The camera was operated in dose-fractionation counting mode with a dose rate of ~16 electrons per A2 s-1, resulting in a total dose of 50 electrons per A2. The frame time was adjusted to 1 frame per 1 electron per A2
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

Particle selectionNumber selected: 6582748
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: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Number images used: 468211
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-9srr:
Full-length cryo-EM structure of essential Mycoplasma pneumoniae lipoprotein Mpn436

PDB-9srv:
Partial cryo-EM structure of essential Mycoplasma pneumoniae lipoprotein Mpn436 (flexible loops excluded)

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