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- EMDB-53144: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pne... -

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Basic information

Entry
Database: EMDB / ID: EMD-53144
TitleHomotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
Map data
Sample
  • Complex: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
    • Protein or peptide: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
KeywordsLipoprotein Mycoplasma pneumoniae PPIase Homotrimer / MEMBRANE PROTEIN
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsManger S / Keles I
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Structure of the essential Mycoplasma pneumoniae lipoprotein Mpn444 reveals a peptidyl-prolyl isomerase domain involved in extracellular protein folding
Authors: Manger S / Keles I / Frangakis AS
History
DepositionMar 14, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53144.png

Downloads & links

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Map

FileDownload / File: emd_53144.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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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

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0368
Minimum - Maximum-0.18538675 - 0.42365777
Average (Standard dev.)-0.000064534535 (±0.009488282)
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_53144_msk_1.map
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Half map: #2

Fileemd_53144_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53144_half_map_2.map
Projections & Slices
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Slices (1/2)
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Sample components

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Entire : Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pne...

EntireName: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
Components
  • Complex: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
    • Protein or peptide: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae

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Supramolecule #1: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pne...

SupramoleculeName: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Macromolecule #1: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pne...

MacromoleculeName: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 117.943305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AQPTASTVEG LFKPSSAFAD RTDFSLSSIL QKSLINRESF NQYLAMRLAP VLRTFYEDNY DTDIKERLNG FTADTDNAFV SQEQNLRNQ FRENYLVHLQ TDIFDNTGGN QAAWKLRDVN NKIIDDFISR IFAKNFVEYV QDGVGPLTKP TKSLIENTSN F KNIKLQPK ...String:
AQPTASTVEG LFKPSSAFAD RTDFSLSSIL QKSLINRESF NQYLAMRLAP VLRTFYEDNY DTDIKERLNG FTADTDNAFV SQEQNLRNQ FRENYLVHLQ TDIFDNTGGN QAAWKLRDVN NKIIDDFISR IFAKNFVEYV QDGVGPLTKP TKSLIENTSN F KNIKLQPK FVNKNAKLKI NNDAVYAAIQ DKLLDQFITN ENPNLVSRVV FTNETPVDGF DNYFNTKVIQ SPTPSYQFQV FN KYNQQSG GTKGANGFNL LASNLKSYKN DQSKGIDIPN KFSSDSGGKL LLKASDMFDT FDPSFSAAFI QGYLALQKKS KGA DSKEVD SLIKDKSIIE NFFVDNNTTV HKTDLVKIFG DKDVFAGEYK QQISKAVVDL IEVKKDSSSQ PDYILSRGKD GIHL MAVDG GSHYLTESGR DVAKQKKFLL FRALQTKYGL VDTDTTYDFK LFDEVKKYFD TNRILFLFEA LLDLSSDTNN KDNFL SYPQ FKKFADSIKS IEKDLKELVQ AHYKQAVFNE TAVAENKVTL KLAERNQPFI DNERNNQIEQ NGLAAKLPYE QDAKTG HYN DLGNYYKDII DNVDKKGNFS EEVVSKLKDN KKKVEEAAKK HVEALKVFTI PSPLYSQVIL VQTKLSFTPE STSLGLN LA LNNYLTSTEL QNSIKLSYFQ EDEAFKKIID ITNLTFSQQS GGTGGTNGNN NLTADNWKIF KETYLLDLFE SQAQKSIF G HVGIEGVLDT LYSSLNLEER LDSDDVIDYL SYLYTAHWLL KDNLKNYKQS LQSKLSRTSN AFLVWSVDSE KNKDNNSDI TQTEVKNPNF VFGSSVYDRY GFRGIVTSST SGSLPEAVSR RLFKQFVNQT NNAYKGALFS FGSMDNLKNI INGIQTQTEF DALYNHLTS DLNIDVTGVD KNKTLTEQKT SLTSFVDSNF KQKDVFSRFD GYIGDNKVEE KNYTSYQFLS DGGKYHATFV K QVNLDDVE KIGTDSLKQE DSSKDKRLNL SLEEFLAAIA LEALDPNNQT QAINALISGN KKGLVKVGDF RIFSSISAQW VR RF

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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 0-0.01 % LMNG or 1 mM CHAPSO
GridModel: Quantifoil R1.2/1.3 / 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
Details: Whatman 595 filter papers were incubated for 1 h in the Vitrobot chamber at 100% relative humidity and 277 K prior to plunge freezing..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 3376184
CTF correctionSoftware - Name: cryoSPARC (ver. v4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Number images used: 506291
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 classificationSoftware - Name: cryoSPARC (ver. v4.5.3)

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