[English] 日本語
Yorodumi
- EMDB-30583: CryoEM structure of cotton cellulose synthase isoform 7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30583
TitleCryoEM structure of cotton cellulose synthase isoform 7
Map data
Sample
  • Complex: Cellulose synthase
    • Protein or peptide: Cellulose synthase
Keywordscellulose synthase / cotton / MEMBRANE PROTEIN
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 / trans-Golgi network / cell wall organization / membrane => GO:0016020 / 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-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesGossypium hirsutum (cotton)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGuan ZY / Xue Y
CitationJournal: Plant Biotechnol J / Year: 2021
Title: Structural insights into homotrimeric assembly of cellulose synthase CesA7 from Gossypium hirsutum.
Authors: Xiangnan Zhang / Yuan Xue / Zeyuan Guan / Chen Zhou / Yangfan Nie / She Men / Qiang Wang / Cuicui Shen / Delin Zhang / Shuangxia Jin / Lili Tu / Ping Yin / Xianlong Zhang /
Abstract: Cellulose is one of the most abundant organic polymers in nature. It contains multiple β-1,4-glucan chains synthesized by cellulose synthases (CesAs) on the plasma membrane of higher plants. CesA ...Cellulose is one of the most abundant organic polymers in nature. It contains multiple β-1,4-glucan chains synthesized by cellulose synthases (CesAs) on the plasma membrane of higher plants. CesA subunits assemble into a pseudo-sixfold symmetric cellulose synthase complex (CSC), known as a 'rosette complex'. The structure of CesA remains enigmatic. Here, we report the cryo-EM structure of the homotrimeric CesA7 from Gossypium hirsutum at 3.5-angstrom resolution. The GhCesA7 homotrimer shows a C3 symmetrical assembly. Each protomer contains seven transmembrane helices (TMs) which form a channel potentially facilitating the release of newly synthesized glucans. The cytoplasmic glycosyltransferase domain (GT domain) of GhCesA7 protrudes from the membrane, and its catalytic pocket is directed towards the TM pore. The homotrimer GhCesA7 is stabilized by the transmembrane helix 7 (TM7) and the plant-conserved region (PCR) domains. It represents the building block of CSCs and facilitates microfibril formation. This structure provides insight into how eukaryotic cellulose synthase assembles and provides a mechanistic basis for the improvement of cotton fibre quality in the future.
History
DepositionSep 26, 2020-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7d5k
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30583.png

Downloads & links

-
Map

FileDownload / File: emd_30583.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-2.101253 - 2.6848257
Average (Standard dev.)-0.00000000000029 (±0.051741306)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 304.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z304.360304.360304.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-2.1012.685-0.000

-
Supplemental data

-
Sample components

-
Entire : Cellulose synthase

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

-
Supramolecule #1: Cellulose synthase

SupramoleculeName: Cellulose synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Gossypium hirsutum (cotton)

-
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: Gossypium hirsutum (cotton)
Molecular weightTheoretical: 118.129711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEASAGLVAG SHNRNELVVI HGHEEPKPLK NLDGQVCEIC GDEIGVTVDG DLFVACNECG FPVCRPCYEY ERREGTQQCP QCKTRYKRL KGSPRVEGDE DEEDVDDIEH EFNIDDEQNK HRNVVESILH GKMSYGRGPE DDETPQIPVI TGVRSRPVSG E FPIAGALA ...String:
MEASAGLVAG SHNRNELVVI HGHEEPKPLK NLDGQVCEIC GDEIGVTVDG DLFVACNECG FPVCRPCYEY ERREGTQQCP QCKTRYKRL KGSPRVEGDE DEEDVDDIEH EFNIDDEQNK HRNVVESILH GKMSYGRGPE DDETPQIPVI TGVRSRPVSG E FPIAGALA YGEHMPNASL HKRVHPYPMS ETEGAERWDD KKEGGWKERM DDWKMQQGNL GPEADDAYDD MSMLDEARQP LS RKVPIAS SKINPYRMVI VARLLILAFF LRYRILNPVH DAIGLWLTSV ICEIWFAFSW ILDQFPKWFP IDRETYLDRL SLR YEREGE PNMLAPVDIF VSTVDPMKEP PLVTANTVLS ILAMDYPVDK ISCYISDDGA SMLTFESLSE TAEFARKWVP FCKK FAIEP RAPEMYFTLK VDYLKDKVQP TFVKERRAMK REYEEFKVRI NALVAKAQKV PPEGWIMQDG TPWPGNNTKD HPGMI QVFL GQSGGHDTEG NELPRLVYVS REKRPGFLHH KKAGAMNALV RVSGVLTNAP FMLNLDCDHY INNSKAAREA MCFLMD PQI GRKVCYVQFP QRFDGIDRHD RYANRNTVFF DINMKGLDGI QGPVYVGTGC VFRRQALYGY EPPKGPKRPK MVSCGCC PC FGRRKKDKKY PKNGGNENGP SLEAVEDDKE LLMSQMNFEK KFGQSAIFVT STLMDQGGVP PSSSPAALLK EAIHVISC G YEDKTEWGSE LGWIYGSITE DILTGFKMHC RGWRSIYCMP KLPAFKGSAP INLSDRLNQV LRWALGSVEI FFSRHCPAW YGLKGAKLRW LERFAYVNTT IYPFTSLPLL AYCTLPAICL LTDKFIMPPI STFASLFFIA LFLSIFATGI LELRWSGVSI EEWWRNEQF WVIGGISAHL FAVVQGLLKV LAGIDTNFTV TSKTTDDEEF GELYTFKWTT LLIPPTTVLI INLVGVVAGI S DAINNGYQ SWGPLFGKLF FSFWVIVHLY PFLKGLMGRQ NRTPTIVVIW SVLLASIFSL LWVRIDPFVL KTKGPDTTQC GI NC

UniProtKB: Cellulose synthase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: RANDOM CONICAL TILT
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: 185759
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

+
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://pdbjlvh1.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