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- EMDB-65074: Complex structure of BoNT-like PG1 at pH 6.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-65074
TitleComplex structure of BoNT-like PG1 at pH 6.0
Map data
Sample
  • Complex: Complex structure of BoNT-like PG1 at pH 6.0
    • Protein or peptide: LC
    • Protein or peptide: HC
  • Ligand: ZINC ION
Keywordstoxin / LC / HC / complex
Biological speciesParaclostridium ghonii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsLiu Z / Chen P
Funding support China, 2 items
OrganizationGrant numberCountry
Other government2024040801020228 China
Other government2024AFB026 China
CitationJournal: Nat Commun / Year: 2026
Title: Structure and functional divergence of the non-canonical BoNT-like toxin PG1 and PG2
Authors: Yang J / Liu Z / Jiang L / Ye X / Chao Y / Ren J / Zhu X / Yang S / Guo X / Zeng J / Wu H / Chen P / Zhang S
History
DepositionJun 17, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65074.png

Downloads & links

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Map

FileDownload / File: emd_65074.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 416 pix.
= 349.44 Å		0.84 Å/pix.
x 416 pix.
= 349.44 Å		0.84 Å/pix.
x 416 pix.
= 349.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0714
Minimum - Maximum-0.37329504 - 0.8443907
Average (Standard dev.)-0.00018459851 (±0.010917195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 349.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65074_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65074_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 : Complex structure of BoNT-like PG1 at pH 6.0

EntireName: Complex structure of BoNT-like PG1 at pH 6.0
Components
  • Complex: Complex structure of BoNT-like PG1 at pH 6.0
    • Protein or peptide: LC
    • Protein or peptide: HC
  • Ligand: ZINC ION

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Supramolecule #1: Complex structure of BoNT-like PG1 at pH 6.0

SupramoleculeName: Complex structure of BoNT-like PG1 at pH 6.0 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Paraclostridium ghonii (bacteria)
Molecular weightTheoretical: 142 KDa

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Macromolecule #1: LC

MacromoleculeName: LC / type: protein_or_peptide / ID: 1
Details: LC(M1 to Q392, containing the double mutations R333A, Y336A) was expressed as a fusion protein with HC via a 14aa linker (GSGSLVPRGSGSGS) at its C-terminal. Residues N219 to E236 and the C- ...Details: LC(M1 to Q392, containing the double mutations R333A, Y336A) was expressed as a fusion protein with HC via a 14aa linker (GSGSLVPRGSGSGS) at its C-terminal. Residues N219 to E236 and the C-terminal linker region are unresolved in the density map, likely due to their flexibility.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paraclostridium ghonii (bacteria) / Strain: strain NCTR 3900
Molecular weightTheoretical: 45.503875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 IGDVRIATRA AVHSEDVTPV EVVDFKNNYK LNSGFLEGQD ISKKYFITNP PKMRRRALRN FKCTIQGSGS LVPR GSGSG S

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Macromolecule #2: HC

MacromoleculeName: HC / type: protein_or_peptide / ID: 2
Details: HC (A2 to A838, with a I5C mutant) was expressed as a fusion protein to the C-term of LC via a 14aa linker (GSGSLVPRGSGSGS). A 6x His tag and two residue (LE) were further added to the HC C- ...Details: HC (A2 to A838, with a I5C mutant) was expressed as a fusion protein to the C-term of LC via a 14aa linker (GSGSLVPRGSGSGS). A 6x His tag and two residue (LE) were further added to the HC C-term to facilitate protein purification. Residues K403 to L413, the C-term 4 residues (F835 to A838), and the His tag regions are unresolved in the density map, likely due to their flexibility.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paraclostridium ghonii (bacteria) / Strain: strain NCTR 3900
Molecular weightTheoretical: 96.716031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ADICASVDKK DVFAVSDTSY FKNFKFPSKK ISDTGEVIDS TKLPQIKDTY KSSREEPIPD NDSTINVKNI TTYHYLEAQK PKNSSIELT MVAPSKSKKP NDCVVEAIND NNKIYTPFSG TAKQFNTVVP IANTAANVIT WLEAIADIFS SETGTFDKLE R AGKETLYY ...String:
ADICASVDKK DVFAVSDTSY FKNFKFPSKK ISDTGEVIDS TKLPQIKDTY KSSREEPIPD NDSTINVKNI TTYHYLEAQK PKNSSIELT MVAPSKSKKP NDCVVEAIND NNKIYTPFSG TAKQFNTVVP IANTAANVIT WLEAIADIFS SETGTFDKLE R AGKETLYY IPYVGQLLSI GENVLIGDFK NALLNTGLII LLDIAPELNI PLLGAFEAYK EYKSLEEFRK AIDNVIDERN KR WHSVYSF VAHQWYGQVN IQIEQRLNHF YQALSYQAGV IKNRVDIEYA RHKEGLEEKE ERKLMWASVD CIGSIEASVK EAT KNAEKF LEKSSILYFK EEILPKVHKN LEEFDKNTLF NIYTNIDEFS NRGIAEISEC KKVEADVNNG FRPIKFDFSL LTNL MKSDS LTDEVILEKA LEDALVFSLG VRNGKIQNLS KKWANLTIGT DIRVVHGRDN ESIRLNSTQD SSIQIEKNTN LRFLD SENF SLSFWIRVPR YNKFDKDKDL NNEYTIVNNM DTATKGFKIS IKNGILLWTL KGTQQKTIEI PLSNTKVSDN IWRHVA IIN NKDGNCTIYV DGAQKNAVSL SGLDEITNTL PITLQLVGNK NKKQFIRLDQ FNIYEKALSQ TEVGKLFSSY FKDSDIR DY WGEPLAYNKT YNMINIAYQG RGLQSTNNKI SLQPKAVFDP TGDGSYIPRL YRGYDVLLQK DSQSKTTDIM PKKDDLIN I KLKSGHNFVG FNSTIDTSQK YLKLTTALLS EVDDPKGFKL MSLKKDNWIQ IKKETWMSKN GNVIPQGLVG KRSVDSDVY LYLWDWETEK DDYSEKQWSF ICQDEGWIDS DGMFTNALEH HHHHH

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration1.3 mg/mL
BufferpH: 6 / Details: 20 mM MES, pH 6.0, 100 mM NaCl.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K
DetailsMonodispers, the LC and HC complex.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsCryo-EM imaging was performed on a Titan Krios G4 electron microscope equipped with a Gatan K3 direct electron detector and a GIF BioQuantum energy filter.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 169973
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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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-9vi0:
Complex structure of BoNT-like PG1 at pH 6.0

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