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- EMDB-63339: Composite map of collagenase H (E416Q mutant) from Hathewaya hist... -

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Basic information

Entry
Database: EMDB / ID: EMD-63339
TitleComposite map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10
Map data
Sample
  • Organelle or cellular component: ColH-(POG)10 complex
    • Protein or peptide: Collagenase ColH
    • Protein or peptide: (Pro-Hyp-Gly)10
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
KeywordsCollagenase / Hathewaya histolytica / Clostridium histolyticum / METAL BINDING PROTEIN
Function / homology
Function and homology information


tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / PKD domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Polycystic kidney disease (PKD) domain profile. ...Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / PKD domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHathewaya histolytica (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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_63339.png

Downloads & links

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Map

FileDownload / File: emd_63339.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.32973522 - 0.5841681
Average (Standard dev.)0.000028869716 (±0.011017265)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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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
    • Protein or peptide: Collagenase ColH
    • Protein or peptide: (Pro-Hyp-Gly)10
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION

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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-#2
Source (natural)Organism: Hathewaya histolytica (bacteria)

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Macromolecule #1: Collagenase ColH

MacromoleculeName: Collagenase ColH / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: microbial collagenase
Source (natural)Organism: Hathewaya histolytica (bacteria)
Molecular weightTheoretical: 112.305172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSVQNESKRY TVSYLKTLNY YDLVDLLVKT EIENLPDLFQ YSSDAKEFYG NKTRMSFIMD EIGRRAPQYT EIDHKGIPTL VEVVRAGFY LGFHNKELNE INKRSFKERV IPSILAIQKN PNFKLGTEVQ DKIVSATGLL AGNETAPPEV VNNFTPILQD C IKNIDRYA ...String:
GSVQNESKRY TVSYLKTLNY YDLVDLLVKT EIENLPDLFQ YSSDAKEFYG NKTRMSFIMD EIGRRAPQYT EIDHKGIPTL VEVVRAGFY LGFHNKELNE INKRSFKERV IPSILAIQKN PNFKLGTEVQ DKIVSATGLL AGNETAPPEV VNNFTPILQD C IKNIDRYA LDDLKSKALF NVLAAPTYDI TEYLRATKEK PENTPWYGKI DGFINELKKL ALYGKINDNN SWIIDNGIYH IA PLGKLHS NNKIGIETLT EVMKVYPYLS MQHLQSADQI KRHYDSKDAE GNKIPLDKFK KEGKEKYCPK TYTFDDGKVI IKA GARVEE EKVKRLYWAS KEVNSQFFRV YGIDKPLEEG NPDDILTMVI YNSPEEYKLN SVLYGYDTNN GGMYIEPEGT FFTY EREAQ ESTYTLEELF RHQYTHYLQG RYAVPGQWGR TKLYDNDRLT WYEEGGAELF AGSTRTSGIL PRKSIVSNIH NTTRN NRYK LSDTVHSKYG ASFEFYNYAC MFMDYMYNKD MGILNKLNDL AKNNDVDGYD NYIRDLSSNY ALNDKYQDHM QERIDN YEN LTVPFVADDY LVRHAYKNPN EIYSEISEVA KLKDAKSEVK KSQYFSTFTL RGSYTGGASK GKLEDQKAMN KFIDDSL KK LDTYSWSGYK TLTAYFTNYK VDSSNRVTYD VVFHGYLPNE GDSKNSLPYG KINGTYKGTE KEKIKFSSEG SFDPDGKI V SYEWDFGDGN KSNEENPEHS YDKVGTYTVK LKVTDDKGES SVSTTTAEIK DLSENKLPVI YMHVPKSGAL NQKVVFYGK GTYDPDGSIA GYQWDFGDGS DFSSEQNPSH VYTKKGEYTV TLRVMDSSGQ MSEKTMKIKI TDPVYPIGTE KEPNNSKETA SGPIVPGIP VSGTIENTSD QDYFYFDVIT PGEVKIDINK LGYGGATWVV YDENNNAVSY ATDDGQNLSG KFKADKPGRY Y IHLYMFNG SYMPYRINIE GSVGR

UniProtKB: Collagenase ColH

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Macromolecule #2: (Pro-Hyp-Gly)10

MacromoleculeName: (Pro-Hyp-Gly)10 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.690828 KDa
SequenceString:
P(HYP)GP(HYP)GP(HYP)GP (HYP)GP(HYP)GP(HYP)GP(HYP) GP(HYP)GP(HYP)GP(HYP)G

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / 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 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: 3.4 Å / Resolution method: OTHER / Number images used: 58438
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9lrm:
Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10

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