[English] 日本語
Yorodumi
- EMDB-19119: CgsiGP3 sample in nanodisc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19119
TitleCgsiGP3 sample in nanodisc
Map data
Sample
  • Complex: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens
    • Protein or peptide: Cyclic beta 1-2 glucan synthetase
  • Ligand: water
Keywordscgs / cyclic glucan / ANTIBIOTIC
Function / homology
Function and homology information


cellobiose phosphorylase / cellobiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process / membrane
Similarity search - Function
NdvB, GH94N domain 1 / NdvB, GH94N domain 2 / Glycoamylase-like, conserved domain / Putative glucoamylase / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain ...NdvB, GH94N domain 1 / NdvB, GH94N domain 2 / Glycoamylase-like, conserved domain / Putative glucoamylase / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Cyclic beta 1-2 glucan synthetase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsSedzicki J / Ni D / Lehmann F / Stahlberg H / Dehio C
Funding support Switzerland, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_201273 Switzerland
Swiss National Science FoundationNCCR AntiResist grant 180541 Switzerland
Swiss National Science FoundationCRSII5_177195 Switzerland
Swiss National Science FoundationSino-Swiss Science and Technology Cooperation SSSTC grant Switzerland
CitationJournal: Nat Commun / Year: 2024
Title: Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens.
Authors: Jaroslaw Sedzicki / Dongchun Ni / Frank Lehmann / Henning Stahlberg / Christoph Dehio /
Abstract: The synthesis of complex sugars is a key aspect of microbial biology. Cyclic β-1,2-glucan (CβG) is a circular polysaccharide critical for host interactions of many bacteria, including major ...The synthesis of complex sugars is a key aspect of microbial biology. Cyclic β-1,2-glucan (CβG) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). CβG is produced by the cyclic glucan synthase (Cgs), a multi-domain membrane protein. So far, its structure as well as the mechanism underlining the synthesis have not been clarified. Here we use cryo-electron microscopy (cryo-EM) and functional approaches to study Cgs from A. tumefaciens. We determine the structure of this complex protein machinery and clarify key aspects of CβG synthesis, revealing a distinct mechanism that uses a tyrosine-linked oligosaccharide intermediate in cycles of polymerization and processing of the glucan chain. Our research opens possibilities for combating pathogens that rely on polysaccharide virulence factors and may lead to synthetic biology approaches for producing complex cyclic sugars.
History
DepositionDec 12, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19119.png

Downloads & links

-
Map

FileDownload / File: emd_19119.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 320 pix.
= 409.984 Å		1.28 Å/pix.
x 320 pix.
= 409.984 Å		1.28 Å/pix.
x 320 pix.
= 409.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2812 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.375
Minimum - Maximum-1.608448 - 3.615556
Average (Standard dev.)0.0021277424 (±0.08637462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 409.984 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_19119_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19119_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens

EntireName: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens
Components
  • Complex: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens
    • Protein or peptide: Cyclic beta 1-2 glucan synthetase
  • Ligand: water

-
Supramolecule #1: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens

SupramoleculeName: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)

-
Macromolecule #1: Cyclic beta 1-2 glucan synthetase

MacromoleculeName: Cyclic beta 1-2 glucan synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: cellobiose phosphorylase
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Molecular weightTheoretical: 313.358656 KDa
SequenceString: DHNDSIRASY MTIEELHDAG AALSRDGADS LPGFMEFDFF ERHRENEKEI LRVYRTTAVD AENGATITPA AEWLLDNHYV IEEAIQEVR RDFPRKFYRQ LPTMTVGGVT IPRVMALGWL YVAHTHSTVS RENMTALVDG YQTSQTLQIG ELWALPSIIR F VLIENLRR ...String:
DHNDSIRASY MTIEELHDAG AALSRDGADS LPGFMEFDFF ERHRENEKEI LRVYRTTAVD AENGATITPA AEWLLDNHYV IEEAIQEVR RDFPRKFYRQ LPTMTVGGVT IPRVMALGWL YVAHTHSTVS RENMTALVDG YQTSQTLQIG ELWALPSIIR F VLIENLRR ISIRVERSRR MRQKANEVVD EIIRLNDAEA SAALLKQVDS LVDDPTFATQ FLYRLRNGSQ TSGFAVAWLE ER LHAAGTD AENVMMSEHN RLASGNVTMG NIVKSLREID DTEWSVWFEE VSHIDKVLRE ETDYEILDFG SRNTYRNTIE LLA RRSPRT EVEVARAAVE MARSDLPAGA DENHRVNVGS VLVGQRRFEL EKALGYRPLA SQHIVRSMRK FNWLAIAAPV LLIT AVAML AVGWFLAKAG MPWYVVTAFL LMFALPASEG ATGLFNTLVT FFVKPFRLVG YEFKNGIPED ARTLVAVPCM LTSRD SVDE MMRNIEVHYL ANPHGEIYFS LVSDWRDAPY EQSDEDLEIL DYAKRELAAL NSRYAFDGKT RFYLLHRRRI YNSAEE CWM GWERKRGKLH ELNMLLRGDK DTTFLGGSNI VPADVKYVMT LDADTRLMRD AVTKLVGKMH HPINRPKIDP VSGRVVE GY GLLQPRVTPS LTTGKDASVF QRVFSINRGI DPYVFTVSDV YQDLTSEGTF TGKGLYDVDA FEAALKGRIE ENSILSHD L LEGSFARCAL VTDVELVEDF PTRYEVEVSR QHRWARGDWQ LLPFIIDRAR GVTAIGRWKM VDNLRRSLTP IAWFFASIL GWYFMDPLGA LIWQILLIFS LFVAPTLSLL SGLVPRSTDI VPQAHFFTIW SEIRATNAQV ALRIVFIADA ACMMTDAIVR SLYRLLVSH KLMLEWRTAA SMQSSAQGSI VDYYRQMWHA PVVAMLGLLF AALPGDNAFL IGIPFTLLWV LSPAVAWYVS Q SAETEDRL FVSEHVSFEL RKIARRTWRY YEAFVTPQEN HLPPDNFQET PEPIVASRTS PTNIGVYLLS VISARQFGWI SF ADTLERI ENTIQTVEKM EKHRGHLYNW YHTDTLQTLG PRYVSAVDSG NLAGHLIAVS SACRDWAEAP SAHLQGNLDG IGD VAGILR ETLKALPDNR KTLRPLHRRL EERIIGFSNA LASVKREHEF ASIRVINLAV LARDIQKLAT NVDHEVKSAQ SAEV TRWAQ LLVESCEAHI SDSAIDLTNM EPLRQRLASL RDRSRNLAFS MDFTFLYRKD RRLLSIGYRV ESKELDEACY DLLAS ECRL TSLFAIAKGD LPTEHWYRLG RQVVPIGAQG ALVSWSGSMF EYLMPPLVMQ ERQGGILNQT NNLIVKEQMN HGRRLG TPW GISEAAFNAR DHNMNYQYTN FGVPTLGLKR GLGQNAVIAP YASILASQYD PDGALENLDK LRKLGALGQY GFHDAVD FT PTRVPDGKVC AVVYNYYAHH HGMSIAAVAN VAFDGVLREL FHSDPVIEAA ELLLQEKAPR EVPVMSAKYE PETPGKEQ A DLLRAEVRSI ADPAVRDREV VFLSNGHYST MLTSTGAGYS KWNGQAISRW KADPTDDRWG TFIFLRDTTN GQWWSATAE PRVIEGEKTK TIFTDDKAEF HKTIGDLQSV VECIVATEHD AEGRRITLLN VGSEDRYIEV TSYMEPVIAS EDDDNAHPLF SRMFVQTEI GRRGDVIRAW RNRRSQNEPG TVIAHLAADN AGPSRPTEFE TDRAKFIGRG RSLREAAAFD AGATLSSSDG F TLDPILSL RRTVRVPAGK KVSVIFWTIA APSREEVDKA IDRYRHPDAF AHELVHAWTR TQVQMRHVGV TSQQAAAFQH LG RYLTYPD MHLRADSETL KTGLASQRAL WPLAISGDFP IFSLRINDDM DMDIAREALS AHEYLRSRGV IFDLVIVNER AAS YAQDMQ HALDHISETQ RRINPADGGR PHVFSVRRDL MDEETWSALL AASRVVLHVR NGKIVDQINR AVSLFAANRG PDGS SDAAQ ARLPVPAFPV AEPVEDAGDL DFWNGFGGFA KNGQEYVVRL NGGQSTPHPW INVISNENFG FHISAEGAGF SWSRN SRDY QLTPWTNDPV INRPGEAFYV ADVETGKLYT PCAALSRDPE AMFETRHGLG YSILTGVADT LEVELTQTVD REKPVK FSQ VIVRNKGSKS RRLKVYAYVE WVLGNNGQKS APFILSRHDA GSNAIFASNP YSIDYSARTS FLTLDSEASG FTTSRRE FI GRFGSAQAPQ GIVAGAALSG TTEVDGDPCA ALMQEIHLKP GEERHMTFIL GDADNAEEAE ALVKDVRQAD FLSVLEES K KFWTGFTGQL QVSTPDAGFN HMVNNWLPYQ ALACRILART AFYQSSGAFG FRDQLQDTLA FLLYQPDLAR TQILRAAGR QFPEGDVQHW WLPLTGAGVR TTISDDVVWL AYAINQYVSA TGDAAILDES IPFLKGPALM PGQHDAFFQP ETSERSATLY EHAALALDL AIHRTGENGL PLILGGDWND GMNRVGVGGK GTSVWLGWFL AGALRDFIEI AEKRGDTDRV GKWASHREKL R HVLETAGW DGSYYRRGYF DDGTPLGSAS SEECQIDSLG QSWSVLSGEG EEGRSRQAMD AVMEHLVDEK TGIIRLFTPP FS RASHDPG YIKGYPPGVR ENGGQYTHAA TWVVLALAKQ GRAQEAWNCF KLLNPVNHAL DAASSETYRV EPYVVTADVY GEG AYAGRG GWSWYTGSAG WLYRAAVEGI LGITRTDGKL HVSPSLPEDW SGFSIRITLD GKARDIAVSR KAGTADVSVS VDG

UniProtKB: Cyclic beta 1-2 glucan synthetase

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98115
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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