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- EMDB-29679: Hybrid aspen cellulose synthase-8 bound to UDP-glucose -

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Basic information

Entry
Database: EMDB / ID: EMD-29679
TitleHybrid aspen cellulose synthase-8 bound to UDP-glucose
Map datasharpened map after local refinement in Cryosparc
Sample
  • Complex: Homotrimeric cellulose synthase complex
    • Protein or peptide: Cellulose synthase
  • Ligand: URIDINE-5'-DIPHOSPHATE-GLUCOSE
  • Ligand: MAGNESIUM ION
KeywordsCellulose / cell wall / UDP / PLANT PROTEIN
Function / homology
Function and homology information


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/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesPopulus tremula x Populus tremuloides (plant) / Populus tremula x P. tremuloides/Amanita muscaria mixed EST library (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsVerma P / Zimmer J
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: bioRxiv / Year: 2023
Title: Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8.
Authors: Preeti Verma / Albert L Kwansa / Ruoya Ho / Yaroslava G Yingling / Jochen Zimmer /
Abstract: Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. ...Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrate's glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loop with the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation.
HIGHLIGHTS: Cryo-EM structures of substrate and product bound poplar cellulose synthase provide insights into substrate selectivitySite directed mutagenesis signifies a critical function of the ...HIGHLIGHTS: Cryo-EM structures of substrate and product bound poplar cellulose synthase provide insights into substrate selectivitySite directed mutagenesis signifies a critical function of the gating loop for catalysisMolecular dynamics simulations support persistent gating loop - substrate interactionsGating loop helps in positioning the substrate molecule to facilitate cellulose elongationConserved cellulose synthesis substrate binding mechanism across the kingdoms.
History
DepositionFeb 4, 2023-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29679.png

Downloads & links

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Map

FileDownload / File: emd_29679.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map after local refinement in Cryosparc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.292084 - 2.098066
Average (Standard dev.)0.0028753849 (±0.051299676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_29679_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_29679_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

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 complex

EntireName: Homotrimeric cellulose synthase complex
Components
  • Complex: Homotrimeric cellulose synthase complex
    • Protein or peptide: Cellulose synthase
  • Ligand: URIDINE-5'-DIPHOSPHATE-GLUCOSE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Homotrimeric cellulose synthase complex

SupramoleculeName: Homotrimeric cellulose synthase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Populus tremula x Populus tremuloides (plant)

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Macromolecule #1: Cellulose synthase

MacromoleculeName: Cellulose synthase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Populus tremula x P. tremuloides/Amanita muscaria mixed EST library (eukaryote)
Molecular weightTheoretical: 112.483023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HHHMMESGAP ICHTCGEQVG HDANGDLFVA CHECNYHICK SCFEYEIKEG RKVCLRCGSP YDENLLDDVE KKGSGNQST MASHLNNSQD VGIHARHISS VSTVDSEMND EYGNPIWKNR VESWKDKRNK KKKSNTKPET EPAQVPPEQQ M ENKPSAEA ...String:
MHHHHHHHHH HHHMMESGAP ICHTCGEQVG HDANGDLFVA CHECNYHICK SCFEYEIKEG RKVCLRCGSP YDENLLDDVE KKGSGNQST MASHLNNSQD VGIHARHISS VSTVDSEMND EYGNPIWKNR VESWKDKRNK KKKSNTKPET EPAQVPPEQQ M ENKPSAEA SEPLSIVYPI PRNKLTPYRA VIIMRLIILG LFFHYRITNP VDSAFGLWLT SVICEIWFAF SWVLDQFPKW KP VNRETFI ERLSARYERE GEPSQLAAVD FFVSTVDPLK EPPLITANTV LSILAVDYPV DKVSCYVSDD GAAMLTFESL VET AEFARK WVPFCKKFSI EPRAPEFYFS QKIDYLKDKV QPSFVKERRA MKRDYEEYKV RVNALVAKAQ KTPDEGWTMQ DGTP WPGNN TRDHPGMIQV FLGNTGARDI EGNELPRLVY VSREKRPGYQ HHKKAGAENA LVRVSAVLTN APYILNLDCD HYVNN SKAV REAMCILMDP QVGRDVCYVQ FPQRFDGIDR SDRYANRNIV FFDVNMKGLD GIQGPMYVGT GCVFNRQALY GYGPPS MPR LRKGKESSSC FSCCCPTKKK PAQDPAEVYR DAKREDLNAA IFNLTEIDNY DDYERSMLIS QLSFEKTFGL SPVFIES TL MENGGVPESA NSSTLIKEAI HVIGCGFEEK TEWGKEIGWI YGSVTEDILS GFKMHCRGWR SIYCMPVRPA FKGSAPIN L SDRLHQVLRW ALGSVEIFFS RHCPFWYGYG GGRLKWLQRL AYINTIVYPF TSLPLIAYCT IPAVCLLTGK FIIPTLSNL ASMLFLGLFI SIIVTAVLEL RWSGVSIEDL WRNEQFWVIG GVSAHLFAVF QGFLKMLAGI DTNFTVTAKA ADDTEFGELY MVKWTTLLI PPTTLLIINI VGVVAGFSDA LNKGYEAWGP LFGKVFFAFW VILHLYPFLK GLMGRQNRTP TIVVLWSVLL T SVFSLVWV KINPFVNKVD NTLAGETCIS IDC

UniProtKB: Cellulose synthase

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Macromolecule #3: URIDINE-5'-DIPHOSPHATE-GLUCOSE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE-GLUCOSE / type: ligand / ID: 3 / Number of copies: 3 / Formula: UPG
Molecular weightTheoretical: 566.302 Da
Chemical component information

ChemComp-UPG:
URIDINE-5'-DIPHOSPHATE-GLUCOSE

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 0.8 µm / Nominal defocus min: 2.3000000000000003 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: EMDB MAP
EMDB ID:

21820

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119285
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.8.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD

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