Database: EMDB / ID: EMD-27655
|Title||Intermediate resolution structure of barley (1,3;1,4)-beta-glucan synthase CslF6.|
|Function / homology||plant-type cell wall organization or biogenesis / Cellulose synthase / Cellulose synthase / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / Nucleotide-diphospho-sugar transferases / membrane => GO:0016020 / Cellulose synthase-like CslF6|
Function and homology information
|Biological species||Hordeum vulgare (barley)|
|Method||single particle reconstruction / cryo EM / Resolution: 4.0 Å|
|Authors||Ho R / Purushotham P / Zimmer J|
|Funding support|| United States, 1 items |
|Citation||Journal: Sci Adv / Year: 2022|
Title: Mechanism of mixed-linkage glucan biosynthesis by barley cellulose synthase-like CslF6 (1,3;1,4)-β-glucan synthase.
Authors: Pallinti Purushotham / Ruoya Ho / Long Yu / Geoffrey B Fincher / Vincent Bulone / Jochen Zimmer /
Abstract: Mixed-linkage (1,3;1,4)-β-glucans, which are widely distributed in cell walls of the grasses, are linear glucose polymers containing predominantly (1,4)-β-linked glucosyl units interspersed with ...Mixed-linkage (1,3;1,4)-β-glucans, which are widely distributed in cell walls of the grasses, are linear glucose polymers containing predominantly (1,4)-β-linked glucosyl units interspersed with single (1,3)-β-linked glucosyl units. Their distribution in cereal grains and unique structures are important determinants of dietary fibers that are beneficial to human health. We demonstrate that the barley cellulose synthase-like CslF6 enzyme is sufficient to synthesize a high-molecular weight (1,3;1,4)-β-glucan in vitro. Biochemical and cryo-electron microscopy analyses suggest that CslF6 functions as a monomer. A conserved "switch motif" at the entrance of the enzyme's transmembrane channel is critical to generate (1,3)-linkages. There, a single-point mutation markedly reduces (1,3)-linkage formation, resulting in the synthesis of cellulosic polysaccharides. Our results suggest that CslF6 monitors the orientation of the nascent polysaccharide's second or third glucosyl unit. Register-dependent interactions with these glucosyl residues reposition the polymer's terminal glucosyl unit to form either a (1,3)- or (1,4)-β-linkage.
Downloads & links
|File||Download / File: emd_27655.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 0.83 Å|
|Symmetry||Space group: 1|
-Half map: #2
|Projections & Slices|
-Half map: #1
-Entire : Barley cellulose synthase-like F6
|Entire||Name: Barley cellulose synthase-like F6|
-Supramolecule #1: Barley cellulose synthase-like F6
|Supramolecule||Name: Barley cellulose synthase-like F6 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all|
|Source (natural)||Organism: Hordeum vulgare (barley)|
-Macromolecule #1: Cellulose synthase-like CslF6
|Macromolecule||Name: Cellulose synthase-like CslF6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO|
|Source (natural)||Organism: Hordeum vulgare (barley)|
|Molecular weight||Theoretical: 105.193797 KDa|
|Recombinant expression||Organism: Spodoptera frugiperda (fall armyworm)|
|Sequence||String: MAPAVAGGGR VRSNEPVAAA AAAPAASGKP CVCGFQVCAC TGSAAVASAA SSLDMDIVAM GQIGAVNDES WVGVELGEDG ETDESGAAV DDRPVFRTEK IKGVLLHPYR VLIFVRLIAF TLFVIWRISH KNPDAMWLWV TSICGEFWFG FSWLLDQLPK L NPINRVPD ...String: |
MAPAVAGGGR VRSNEPVAAA AAAPAASGKP CVCGFQVCAC TGSAAVASAA SSLDMDIVAM GQIGAVNDES WVGVELGEDG ETDESGAAV DDRPVFRTEK IKGVLLHPYR VLIFVRLIAF TLFVIWRISH KNPDAMWLWV TSICGEFWFG FSWLLDQLPK L NPINRVPD LAVLRQRFDR PDGTSTLPGL DIFVTTADPI KEPILSTANS VLSILAADYP VDRNTCYVSD DSGMLLTYEA LA ESSKFAT LWVPFCRKHG IEPRGPESYF ELKSHPYMGR AQDEFVNDRR RVRKEYDEFK ARINSLEHDI KQRNDGYNAA IAH SQGVPR PTWMADGTQW EGTWVDASEN HRRGDHAGIV LVLLNHPSHR RQTGPPASAD NPLDLSGVDV RLPMLVYVSR EKRP GHDHQ KKAGAMNALT RASALLSNSP FILNLDCDHY INNSQALRAG ICFMVGRDSD TVAFVQFPQR FEGVDPTDLY ANHNR IFFD GTLRALDGMQ GPIYVGTGCL FRRITVYGFD PPRINVGGPC FPRLAGLFAK TKYEKPGLEM TTAKAKAAPV PAKGKH GFL PLPKKTYGKS DAFVDTIPRA SHPSPYAAAA EGIVADEATI VEAVNVTAAA FEKKTGWGKE IGWVYDTVTE DVVTGYR MH IKGWRSRYCS IYPHAFIGTA PINLTERLFQ VLRWSTGSLE IFFSKNNPLF GSTYLHPLQR VAYINITTYP FTAIFLIF Y TTVPALSFVT GHFIVQRPTT MFYVYLGIVL STLLVIAVLE VKWAGVTVFE WFRNGQFWMT ASCSAYLAAV CQVLTKVIF RRDISFKLTS KLPSGDEKKD PYADLYVVRW TPLMITPIII IFVNIIGSAV AFAKVLDGEW THWLKVAGGV FFNFWVLFHL YPFAKGILG KHGKTPVVVL VWWAFTFVIT AVLYINIPHM HTSGGKHTTV HGHHGKKLVD TGLYGWLH
|Processing||single particle reconstruction|
|Vitrification||Cryogen name: ETHANE|
|Microscope||FEI TITAN KRIOS|
|Electron beam||Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN|
|Electron optics||Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm|
|Image recording||Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2|
Model: Titan Krios / Image courtesy: FEI Company
|Startup model||Type of model: OTHER / Details: AlphaFold2 predicted structure|
|Initial angle assignment||Type: NOT APPLICABLE|
|Final angle assignment||Type: NOT APPLICABLE|
|Final reconstruction||Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80347|
-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
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
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+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
+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.
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