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- EMDB-21820: Structure of homotrimeric poplar cellulose synthase isoform 8 -

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Basic information

Entry
Database: EMDB / ID: EMD-21820
TitleStructure of homotrimeric poplar cellulose synthase isoform 8
Map dataMap after local refinement and B-factor sharpening (-93).
Sample
  • Complex: CesA
    • Protein or peptide: Cellulose synthase
KeywordsCellulose / polysaccharide / cell wall / glycosyltransferase / membrane protein / translocation
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZimmer J / Pallinti P
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DESC0001090 United States
CitationJournal: Science / Year: 2020
Title: Architecture of a catalytically active homotrimeric plant cellulose synthase complex.
Authors: Pallinti Purushotham / Ruoya Ho / Jochen Zimmer /
Abstract: Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers ...Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA's N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.
History
DepositionApr 19, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wlb
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21820.png

Downloads & links

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Map

FileDownload / File: emd_21820.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap after local refinement and B-factor sharpening (-93).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 340 pix.
= 367.2 Å		1.08 Å/pix.
x 340 pix.
= 367.2 Å		1.08 Å/pix.
x 340 pix.
= 367.2 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 EMDB: 0.17 / Movie #1: 0.25
Minimum - Maximum-1.4841286 - 2.2207265
Average (Standard dev.)-0.00034540455 (±0.045663442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 367.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z367.200367.200367.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-1.4842.221-0.000

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Supplemental data

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Sample components

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Entire : CesA

EntireName: CesA
Components
  • Complex: CesA
    • Protein or peptide: Cellulose synthase

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Supramolecule #1: CesA

SupramoleculeName: CesA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Poplar cellulose synthase containing a nascent cellulose chain
Source (natural)Organism: Populus tremula x Populus tremuloides (plant)
Molecular weightTheoretical: 110 kDa/nm

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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: Populus tremula x Populus tremuloides (plant)
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11532 / Average exposure time: 3.96 sec. / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.25 µm / Nominal defocus min: -0.75 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65665
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6wlb:
Structure of homotrimeric poplar cellulose synthase isoform 8

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