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- EMDB-44266: Cryo-EM structure and molecular assembly of the BoNT-like toxin P... -

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Basic information

Entry
Database: EMDB / ID: EMD-44266
TitleCryo-EM structure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii
Map datastructure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii
Sample
  • Complex: Cryo-EM structure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii
    • Protein or peptide: PG1 light chain
    • Protein or peptide: PG1 heavy chain
KeywordsPG toxin / TOXIN
Biological speciesParaclostridium ghonii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYin L / Dong M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132387 United States
CitationJournal: To Be Published
Title: Cryo-EM structure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii
Authors: Yin L / Dong M
History
DepositionMar 25, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44266.png

Downloads & links

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Map

FileDownload / File: emd_44266.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.46025863 - 0.7518389
Average (Standard dev.)0.00059431244 (±0.022871064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44266_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_44266_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_44266_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure and molecular assembly of the BoNT-like toxin P...

EntireName: Cryo-EM structure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii
Components
  • Complex: Cryo-EM structure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii
    • Protein or peptide: PG1 light chain
    • Protein or peptide: PG1 heavy chain

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Supramolecule #1: Cryo-EM structure and molecular assembly of the BoNT-like toxin P...

SupramoleculeName: Cryo-EM structure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: BoNT-like toxin PG1 complex from Paeniclostridium ghonii
Source (natural)Organism: Paraclostridium ghonii (bacteria)

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Macromolecule #1: PG1 light chain

MacromoleculeName: PG1 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paraclostridium ghonii (bacteria)
Molecular weightTheoretical: 44.494844 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString: MIPINIKDFN YSDPVNNQDI ILVKNEKGSF DKGFFVADKI LLVPARYGNI STDEGGITSK KEKAHVDKKI YLETDSEKNE YLKNMTTLL KRMNSYSTGN KLLNLIIKGE PIYSKDLQGK FIEQTPSRYL DTNTGKRRVN VMITGPGSNV LTKKCTHNGM G LENDPNGK ...String:
MIPINIKDFN YSDPVNNQDI ILVKNEKGSF DKGFFVADKI LLVPARYGNI STDEGGITSK KEKAHVDKKI YLETDSEKNE YLKNMTTLL KRMNSYSTGN KLLNLIIKGE PIYSKDLQGK FIEQTPSRYL DTNTGKRRVN VMITGPGSNV LTKKCTHNGM G LENDPNGK HSNGTGILST IEFSPNYLIA YNKCVADPVL TLFHELVHSM HNLYGIAFPD NVKVPYNALK DKNLVSGEEA LS EILTFGG KDLTTEHLET LWKKLAETVI IVKDFVKTDT QAKDVFLNNL RFLSKNENIK IDTIEDIVNG TLKIKNNISN LTE CEFCKE IGDVRIRTRY AVHSEDVTPV EVVDFKNNYK LNSGFLEGQD ISKKYFITNP PKMRRRALRN FKCTIQ

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Macromolecule #2: PG1 heavy chain

MacromoleculeName: PG1 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paraclostridium ghonii (bacteria)
Molecular weightTheoretical: 95.786078 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString: MADIIASVDK KDVFAVSDTS YFKNFKFPSK KISDTGEVID STKLPQIKDT YKSSREEPIP DNDSTINVKN ITTYHYLEAQ KPKNSSIEL TMVAPSKSKK PNDCVVEAIN DNNKIYTPFS GTAKQFNTVV PIANTAANVI TWLEAIADIF SSETGTFDKL E RAGKETLY ...String:
MADIIASVDK KDVFAVSDTS YFKNFKFPSK KISDTGEVID STKLPQIKDT YKSSREEPIP DNDSTINVKN ITTYHYLEAQ KPKNSSIEL TMVAPSKSKK PNDCVVEAIN DNNKIYTPFS GTAKQFNTVV PIANTAANVI TWLEAIADIF SSETGTFDKL E RAGKETLY YIPYVGQLLS IGENVLIGDF KNALLNTGLI ILLDIAPELN IPLLGAFEAY KEYKSLEEFR KAIDNVIDER NK RWHSVYS FVAHQWYGQV NIQIEQRLNH FYQALSYQAG VIKNRVDIEY ARHKEGLEEK EERKLMWASV DCIGSIEASV KEA TKNAEK FLEKSSILYF KEEILPKVHK NLEEFDKNTL FNIYTNIDEF SNRGIAEISE CKKVEADVNN GFRPIKFDFS LLTN LMKSD SLTDEVILEK ALEDALVFSL GVRNGKIQNL SKKWANLTIG TDIRVVHGRD NESIRLNSTQ DSSIQIEKNT NLRFL DSEN FSLSFWIRVP RYNKFDKDKD LNNEYTIVNN MDTATKGFKI SIKNGILLWT LKGTQQKTIE IPLSNTKVSD NIWRHV AII NNKDGNCTIY VDGAQKNAVS LSGLDEITNT LPITLQLVGN KNKKQFIRLD QFNIYEKALS QTEVGKLFSS YFKDSDI RD YWGEPLAYNK TYNMINIAYQ GRGLQSTNNK ISLQPKAVFD PTGDGSYIPR LYRGYDVLLQ KDSQSKTTDI MPKKDDLI N IKLKSGHNFV GFNSTIDTSQ KYLKLTTALL SEVDDPKGFK LMSLKKDNWI QIKKETWMSK NGNVIPQGLV GKRSVDSDV YLYLWDWETE KDDYSEKQWS FICQDEGWID SDGMFTNA

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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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPEs4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClsodium chloride
GridMaterial: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 53.19 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 364136
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.4.1)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9b6m:
Cryo-EM structure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii

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