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- EMDB-53102: Structure of the GH13 domain of Ruminococcus bromii Amy16 -

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Basic information

Entry
Database: EMDB / ID: EMD-53102
TitleStructure of the GH13 domain of Ruminococcus bromii Amy16
Map data
Sample
  • Complex: Ruminococcus bromii Amy16
    • Protein or peptide: Ruminococcus bromii Amy16
KeywordsGH13 / Ruminococcus bromii / Amy16 / HYDROLASE
Biological speciesRuminococcus bromii L2-63 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsWimmer BH / Medalia O
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation10000885 Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon.
Authors: Benedikt H Wimmer / Sarah Moraïs / Itai Amit / Omar Tovar-Herrera / Meltem Tatli / Anke Trautwein-Schult / Barbara Pfister / Ran Zalk / Paloma Tödtli / Sebastian Simoni / Matteo Lisibach / ...Authors: Benedikt H Wimmer / Sarah Moraïs / Itai Amit / Omar Tovar-Herrera / Meltem Tatli / Anke Trautwein-Schult / Barbara Pfister / Ran Zalk / Paloma Tödtli / Sebastian Simoni / Matteo Lisibach / Liron Levin / Dörte Becher / Edward A Bayer / Ohad Medalia / Itzhak Mizrahi /
Abstract: Degradation of complex dietary fiber by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant ...Degradation of complex dietary fiber by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant starch (RS) degrader in humans, which relies on the amylosome, a specialized cell-bound enzymatic complex. To unravel its architecture, function, and the interplay among its components, we applied a holistic multilayered approach: Cryo-electron tomography reveals that the amylosome comprises a constitutive extracellular layer extending toward the RS substrate. Proteomics demonstrates remodeling of its contents across different growth conditions, with Amy4 and Amy16 comprising 60% of the amylosome in response to RS. Structural and biochemical analyses reveal complementarity and synergistic RS degradation by these enzymes. We demonstrate that amylosome composition and RS degradation are regulated at two levels: structural constraints and expression-driven shifts in enzyme proportions enforce enzyme proximity, which allows R. bromii to fine-tune its adaptation to dietary fiber and shape colonic metabolism.
History
DepositionMar 11, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53102.png

Downloads & links

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Map

FileDownload / File: emd_53102.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 128 pix.
= 166.4 Å		1.3 Å/pix.
x 128 pix.
= 166.4 Å		1.3 Å/pix.
x 128 pix.
= 166.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.08039449 - 0.4757607
Average (Standard dev.)0.0007392526 (±0.013314517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 166.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53102_msk_1.map
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Half map: #2

Fileemd_53102_half_map_1.map
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Half map: #1

Fileemd_53102_half_map_2.map
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Sample components

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Entire : Ruminococcus bromii Amy16

EntireName: Ruminococcus bromii Amy16
Components
  • Complex: Ruminococcus bromii Amy16
    • Protein or peptide: Ruminococcus bromii Amy16

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Supramolecule #1: Ruminococcus bromii Amy16

SupramoleculeName: Ruminococcus bromii Amy16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ruminococcus bromii L2-63 (bacteria)
Molecular weightTheoretical: 93.2 KDa

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Macromolecule #1: Ruminococcus bromii Amy16

MacromoleculeName: Ruminococcus bromii Amy16 / type: protein_or_peptide / ID: 1
Details: removal of signalling peptide for secretion, addition of N-terminal 6x His-Tag
Number of copies: 1 / Enantiomer: LEVO / EC number: alpha-amylase
Source (natural)Organism: Ruminococcus bromii L2-63 (bacteria)
Molecular weightTheoretical: 93.288805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHAE SSPTVSANKY KLKDNIQDGV ILHCFDWTYN DIKAELPKIA KAGFTSIQTS PAQPNGTGTW YWLYQPISFS IGTNGVGTK AELQSLCDEA DKYGIKIIVD VVANHLRGDH NNIDNDLKPS EYWHTFGGGI DWKNRWQVTH GSIGMPDIAT E NPYVQQKV ...String:
MAHHHHHHAE SSPTVSANKY KLKDNIQDGV ILHCFDWTYN DIKAELPKIA KAGFTSIQTS PAQPNGTGTW YWLYQPISFS IGTNGVGTK AELQSLCDEA DKYGIKIIVD VVANHLRGDH NNIDNDLKPS EYWHTFGGGI DWKNRWQVTH GSIGMPDIAT E NPYVQQKV CNYVQELKSV GVDGLRWDAA KHIGVPSEGD DFWKSVTQYG LYNYGEILGG PDDRSTGNED IMKEYTDYIS VT DSNYGKE LRDSFNSGKA PTSSGNWSEK GISNDKLLYW GESHDTWSNN KDWGFSNEMS QNVIDRAYAV AASRNKVTAL YFS RPSSTN KESIKMGEKG STHFTSSEVA QINKFHNAMD GKADYYTVSD GCSVITRKDG GAVIVKGSGS GEVSVENGGG YAKP GTYTD AVSGNTFTIT SSTISGTIGS SGIAVVYDAE PEGPSASVTP GSTNYNTDEL TLTLNCKYAK NAQYSIDDGA FVNYT NGQK ITIGTNLDYD TVTTVTVKAS DGKTTSDPET YTYTKVDPNA VKVVAYDNSS TKWSKVNAYF WSDDNKEMTS WPGKKM TDK GNNIFDIEVP DGAKYVIFNN GDSQTDDLRI ADGNKIYSNG SWQNYSTVKP TQPTTAPSTT VRPTTIATQP TTSQPTT TQ PTTTQPATTQ PATTQPSTTQ PVTEPSNRIL IGDVDLNGTI TVCDSTEVQR YIACISTLSD EALIAADVNK DSVISVKD A TMIQAYIVKL IVEDSYCGTY TENVAPTQPT TNVTEPTTEP TSIQTKNYVY FNNTENWSTV NVYVWSSKDS TYMSWPGMA MESIGNNTYR FELPNGADYA IFNNGSTQTG DLKIPDVNMI YSNGQWSKYS K

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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

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMNH2C(CH2OH)3Tris
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
10.0 mMCaCl2calcium chloride
2.0 mMC4H10O2S2DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 29000 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22073062
CTF correctionSoftware - Name: cryoSPARC / Software - details: blob picker / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 354079
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC / Details: cryoSPARC ab initio
Final angle assignmentType: OTHER / Software - Name: cryoSPARC / Details: cryoSPARC ab initio
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: full-length construct
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9qf9:
Structure of the GH13 domain of Ruminococcus bromii Amy16

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