[English] 日本語
Yorodumi
- EMDB-29678: Hybrid aspen cellulose synthase-8 bound to UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29678
TitleHybrid aspen cellulose synthase-8 bound to UDP
Map dataautosharpened map local refinement in cryosparc
Sample
  • Complex: Homotrimeric cellulose synthase complex
    • Protein or peptide: Cellulose synthase
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
Function / homology
Function and homology information


cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / cell wall organization / metal 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: 3.3 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 3, 2023-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29678.png

Downloads & links

-
Map

FileDownload / File: emd_29678.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationautosharpened map local refinement in cryosparc
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy EMDB: 5.8
Minimum - Maximum-22.75121 - 39.503883
Average (Standard dev.)-2.9795732e-13 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map

Fileemd_29678_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_29678_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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
  • Ligand: MAGNESIUM ION
  • Ligand: water

-
Supramolecule #1: Homotrimeric cellulose synthase complex

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

-
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

-
Macromolecule #3: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM / Uridine diphosphate

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 15.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21820

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.8.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188722

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more