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- EMDB-43245: Cryo EM structure of a soybean CesA6 homotrimer -

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Basic information

Entry
Database: EMDB / ID: EMD-43245
TitleCryo EM structure of a soybean CesA6 homotrimer
Map dataSingle particle cryo EM map after non-uniform (C3) and local refinement in cryoSPARC.
Sample
  • Complex: Homotrimeric cellulose synthase 6
    • Protein or peptide: Cellulose synthase
KeywordsCellulose / glycosyltransferase / microfibril / TRANSFERASE
Function / homology
Function and homology information


cellulose synthase activity / plant-type primary cell wall biogenesis / cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / cell wall organization / zinc ion binding / plasma membrane
Similarity search - Function
Cellulose synthase, RING-type zinc finger / Zinc-binding RING-finger / Cellulose synthase / Cellulose synthase / Nucleotide-diphospho-sugar transferases / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesGlycine max (soybean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHo R / Palliniti P / Zimmer J
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Elife / Year: 2025
Title: Structure, function and assembly of soybean primary cell wall cellulose synthases.
Authors: Ruoya Ho / Pallinti Purushotham / Louis F L Wilson / Yueping Wan / Jochen Zimmer /
Abstract: Plant cell walls contain a meshwork of cellulose fibers embedded into a matrix of other carbohydrate and non-carbohydrate-based biopolymers. This composite material exhibits extraordinary properties, ...Plant cell walls contain a meshwork of cellulose fibers embedded into a matrix of other carbohydrate and non-carbohydrate-based biopolymers. This composite material exhibits extraordinary properties, from stretchable and pliable cell boundaries to solid protective shells. Cellulose, a linear glucose polymer, is synthesized and secreted across the plasma membrane by cellulose synthase (CesA), of which plants express multiple isoforms. Different subsets of CesA isoforms are necessary for primary and secondary cell wall biogenesis. Here, we structurally and functionally characterize the (soybean) primary cell wall CesAs CesA1, CesA3, and CesA6. The CesA isoforms exhibit robust in vitro catalytic activity. Cryo-electron microscopy analyses reveal their assembly into homotrimeric complexes in vitro in which each CesA protomer forms a cellulose-conducting transmembrane channel with a large lateral opening. Biochemical and co-purification analyses demonstrate that different CesA isoforms interact in vitro, leading to synergistic cellulose biosynthesis. Interactions between CesA trimers are only observed between different CesA isoforms and require the class-specific region (CSR). The CSR forms a hook-shaped extension of CesA's catalytic domain at the cytosolic water-lipid interface. Negative stain and cryo-electron microscopy analyses of mixtures of different CesA isoform trimers reveal their side-by-side arrangement into loose clusters. Our data suggest a model by which CesA homotrimers of different isoforms assemble into cellulose synthase complexes to synthesize and secrete multiple cellulose chains for microfibril formation. Inter-trimer interactions are mediated by fuzzy interactions between their CSR extensions.
History
DepositionJan 2, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43245.png

Downloads & links

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Map

FileDownload / File: emd_43245.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle particle cryo EM map after non-uniform (C3) and local refinement in cryoSPARC.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.6732891 - 2.49452
Average (Standard dev.)0.000045479093 (±0.03770988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_43245_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_43245_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Homotrimeric cellulose synthase 6

EntireName: Homotrimeric cellulose synthase 6
Components
  • Complex: Homotrimeric cellulose synthase 6
    • Protein or peptide: Cellulose synthase

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Supramolecule #1: Homotrimeric cellulose synthase 6

SupramoleculeName: Homotrimeric cellulose synthase 6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Glycine max (soybean)

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Macromolecule #1: Cellulose synthase

MacromoleculeName: Cellulose synthase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: cellulose synthase (UDP-forming)
Source (natural)Organism: Glycine max (soybean)
Molecular weightTheoretical: 121.637023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDTKGRLVAG SHNRNEFVLI NADETARVAV TELSGQICQI CGDELEVTVN GEPFVACNEC AFPVCRPCYE YERREGNQVC PQCKTRYKR IKGSPRVEGD EEEDDSDDLE SEFDIGSVFS ARLNYGSQVN GSVIHAPSEF DAASVASEIP LLTYGQEDVG I SADKHALI ...String:
MDTKGRLVAG SHNRNEFVLI NADETARVAV TELSGQICQI CGDELEVTVN GEPFVACNEC AFPVCRPCYE YERREGNQVC PQCKTRYKR IKGSPRVEGD EEEDDSDDLE SEFDIGSVFS ARLNYGSQVN GSVIHAPSEF DAASVASEIP LLTYGQEDVG I SADKHALI LPPFTARGKR VHPMPFPDSS VPVQPRPMDP KKDIAVYGYG SVAWKERMED WKKKQSEKLQ VVRHEGGKDS DE LDDPDLP KMDEGRQPLW RKLPISSSRI NPYRIIIVLR IAILCLFFHY RILHPVNDAY ALWLTSVICE IWFAVSWIFD QFP KWSPIL RETYLDRLSL RYEKEGKPSL LADIDVFVST VDPMKEPPLI TANTVLSILA VDYPVDKVAC YVSDDGAAML TFEA LSETS EFARKWVPFC KKFCIEPRAP EWYFAQKVDY LKDKVDATFI RERRAIKREY EEFKVRINAL VALAQKVPED GWTMQ DGTP WPGNNVRDHP GMIQVFLGQN GVRDIEGNEL PRLVYVSREK RPGYDHHKKA GAMNALVRVS AIITNAPYVL NVDCDH YIN NSKALREAMC FMMDPTSGKK ICYVQFPQRF DGIDRHDRYS NRNVVFFDIN MKGLDGIQGP IYVGTGCVFR RQAFYGY DA PTSKKAPRKT CNCWPKWCCC LCCGSKKKKI KAKSSVKKKI KNKDDIKQMH ALENIEEGIE GIDNEKSSLM SQSKFEKK F GQSSVFIAST LLEDGGVPKA ASSATLLKEA IHVISCGYED KTEWGKEVGW IYGSVTEDIL TGFKMHCHGW RSVYCMPKR PAFKGSAPIN LSDRLHQVLR WALGSVEIFF SRHCPIWYGY GGGLKSLERF SYINSVVYPL TSIPLIAYCA LPAVCLLTGK FIVPEISNY ASIIFMALFI SIAATGILEM QWGGVGIHDW WRNEQFWVIG GASSHLFALF QGLLKVLAGV NTNFTVTSKA A DDGEFADL YIFKWTSLLI PPLTLLIINI IGVIVGVSDA INNGYDSWGP LFGRLFFALW VIVHLYPFLK GVMGKQEGVP TI ILVWAIL LSSILTLLWV RINPFLAKSD VVLEICGLNC D

UniProtKB: Cellulose synthase

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold generated
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192666
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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