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- EMDB-63336: Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histol... -

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Basic information

Entry
Database: EMDB / ID: EMD-63336
TitleCryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10 - focused map of ColH bound to the N-terminal region of collagen model peptide
Map data
Sample
  • Organelle or cellular component: ColH-(POG)10 complex
KeywordsCollagenase / Hathewaya histolytica / Clostridium histolyticum / METAL BINDING PROTEIN
Biological speciesHathewaya histolytica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsOki H / Kawahara K
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
Japan Society for the Promotion of Science (JSPS)24K10218 Japan
Japan Society for the Promotion of Science (JSPS)23K14519 Japan
CitationJournal: Nat Commun / Year: 2026
Title: Bacterial collagenase harnesses collagen geometry for processive cleavage.
Authors: Hiroya Oki / Katsuki Takebe / Adjoa Bonsu / Kazunori Fujii / Ryo Masuda / Nicholas Henderson / Takehiko Mima / Takaki Koide / Mahmoud Moradi / Osamu Matsushita / Joshua Sakon / Kazuki Kawahara /
Abstract: Collagen, the major structural protein in the animal extracellular matrix, forms a triple helix that resists proteolysis and requires specialised enzymes for degradation. Flesh-eating bacteria ...Collagen, the major structural protein in the animal extracellular matrix, forms a triple helix that resists proteolysis and requires specialised enzymes for degradation. Flesh-eating bacteria secrete collagenases that unwind the collagen triple helix and processively trim Gly-X-Y triplet repeats, yet the molecular basis of this process has remained obscure. Here, cryo-electron microscopy reveals how Hathewaya histolytica collagenase ColH engages its substrate and exploits the helix's architecture for catalysis. ColH encircles a single collagen triple helix in a closed-ring conformation and, through dynamic domain motions, dehydrates and destabilises it. The enzyme undergoes substrate-assisted twisting to adopt a rigid ratcheted conformation, in which one chain is bent into a tripeptide-long 'bight' and threaded into the active site for cleavage, while two uncut strands are partitioned to non-catalytic sites. Release of the bight appears to reset the enzyme, with the uncut strands serving as guiding tracks. Repeated cycling between dynamic and rigid states likely enables triplet-by-triplet translocation, allowing ColH to harness collagen's geometry for processive degradation. These findings reveal a bacterial strategy for collagen unwinding and cleavage distinct from that of mammalian collagenases, highlighting divergent evolutionary solutions for degrading one of nature's most intractable substrates.
History
DepositionJan 31, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63336.png

Downloads & links

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Map

FileDownload / File: emd_63336.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.06868859 - 0.1631433
Average (Standard dev.)-0.00007629148 (±0.003552276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63336_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_63336_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63336_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : ColH-(POG)10 complex

EntireName: ColH-(POG)10 complex
Components
  • Organelle or cellular component: ColH-(POG)10 complex

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Supramolecule #1: ColH-(POG)10 complex

SupramoleculeName: ColH-(POG)10 complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Hathewaya histolytica (bacteria)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58438
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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