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- EMDB-55131: Cryo-EM focused map of essential Mycoplasma pneumoniae lipoprotei... -

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Basic information

Entry
Database: EMDB / ID: EMD-55131
TitleCryo-EM focused map of essential Mycoplasma pneumoniae lipoprotein Mpn444 tip region at 4.07 A
Map data
Sample
  • Complex: Essential Mycoplasma pneumoniae lipoprotein Mpn436
    • Protein or peptide: Essential Mycoplasma pneumoniae lipoprotein Mpn436
KeywordsPPIase Chaperone Mycoplasma pneumoniae lipoprotein / CHAPERONE
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.07 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 24, 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_55131.png

Downloads & links

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Map

FileDownload / File: emd_55131.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: 0.341
Minimum - Maximum-3.077568 - 3.3579264
Average (Standard dev.)-0.000018856716 (±0.02353077)
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_55131_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_55131_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 Mpn436

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

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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: Essential Mycoplasma pneumoniae lipoprotein Mpn436

MacromoleculeName: Essential Mycoplasma pneumoniae lipoprotein Mpn436 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKFLRKPQF WLLTLGGFLS TSVILAACAT PSNSALQTVF KARSSQFFNG EQGSLQSALT TALKNPVANK QFIAAPLLKA LEAWYENNED KKITQFLKDT KSNVDSQYTT AVDKVVSASR NKSLFVQQD LLDNAGGSEA TWKAQKLLEQ LISDFASRVF QKNYLNYKKD ...String:
MKKFLRKPQF WLLTLGGFLS TSVILAACAT PSNSALQTVF KARSSQFFNG EQGSLQSALT TALKNPVANK QFIAAPLLKA LEAWYENNED KKITQFLKDT KSNVDSQYTT AVDKVVSASR NKSLFVQQD LLDNAGGSEA TWKAQKLLEQ LISDFASRVF QKNYLNYKKD GQVSTGPFTY D ELHKEESW KNFEFSAPRF SETNDDFFAK IQSQVFDQWV EYTDPTLISQ VNYKYSAPSQ GL GQIYNRE KLKDKLTPSY AFPFFAEEKD IAPNQNVGNK RWKQLVKGEG AITDNNIGQS GTN SQKTGL LKYRNESNKG DFLDFPLNLS DTNETKQLVD ASNIVDQLEA ANLGAALNLK LQVF EQDND ELPQIKELKE DLNNTIVVDK SKDVEKASKT NALFYNDQEG KQQQSDSDPI AGALD DIFA QNTSEGTNLS KLAEQVKKAA ATKMEAKTAV LRTNNSKGQQ NNYVVLDAAI PTFNST TSK SKNNSASNEV LVALKSGSIN LRQVQQTDQN SYSPIKFRIV RNSTGVTVFG LDGGSYY LK QDSTNKKSVS KQSLTLLTKS SSGNSNKVLR DLDKQKQFLK FRAFQAKTNT FYSTNFAF S FPLNETLKSW FDKHRELILA NALVNASLDQ KDKASKALTE AFNPYKELIK EFAPVALAT TMISFYFDQM KALNNKLLER ARNLNQNVNQ ANPTPWLNGL SAKLPYVNTN GNYEKLNNYF TFLITKTLW PKVGQEETSI SEESNKLKTK TADVDKIRDK ILENIQTKVN DFVKNKLKPA L APRPAYSN VILLNVNNDK VLSSGANWSL ASLLQSDKVN PLSFMLLKQA FDNNDLFKKA QK LFKDIQE KSSNNGGMQS SSTTNSDADA LSKVIGNYYY TTWAKLTDKS IYGNPKDNKF DEL FKLAFE ASIDEKSFNV DYKAVIDHYR FIYTLQWLVD QKLKNFKSLL KTNLKFGEVA FIAY KNTET TNFSNPQGVF GSYFNYENSA SEVKESTQTL DPNNFFYKTT TKPTVQAIQQ VASLA LVQK QQMQQNSTDH YGFTGLSTST SSMFDASSRD AILQQITKTS LQQYGSKDQL KKIIQG TNN QLLLDRIAVQ LSGLNPSTTN GGSGKTIATY FQVDAVGNPT LDFQAKRKLL LDLLDQY QN YFGNGAQKSQ RDSTPSGTGN YLTYQNGSDK YTYTQFTYQD IDSLSLTTTS GTNNKIAS D VVAALLLFQA ADKGTQQLAL SAINKPQLNI GDKRIESGLK LLK

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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: 4.07 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

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