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- EMDB-19114: WT-CGS sample in nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-19114
TitleWT-CGS sample in nanodisc
Map data
Sample
  • Complex: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens
    • Protein or peptide: Cyclic beta-(1,2)-glucan synthase NdvB
  • Ligand: URIDINE-5'-DIPHOSPHATE-GLUCOSE
Keywordscgs / cyclic glucan / ANTIBIOTIC
Function / homology
Function and homology information


glycosyltransferase 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 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose mutarotase-like domain superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Cyclic beta-(1,2)-glucan synthase NdvB
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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

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Structure visualization

Supplemental images

emd_19114.png

Downloads & links

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Map

FileDownload / File: emd_19114.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 300 pix.
= 394.8 Å		1.32 Å/pix.
x 300 pix.
= 394.8 Å		1.32 Å/pix.
x 300 pix.
= 394.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.316 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.30495772 - 0.63722056
Average (Standard dev.)0.000008446075 (±0.019264724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 394.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_19114_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19114_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19114_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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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 synthase NdvB
  • Ligand: URIDINE-5'-DIPHOSPHATE-GLUCOSE

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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)

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Macromolecule #1: Cyclic beta-(1,2)-glucan synthase NdvB

MacromoleculeName: Cyclic beta-(1,2)-glucan synthase NdvB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Molecular weightTheoretical: 315.448031 KDa
Recombinant expressionOrganism: Agrobacterium tumefaciens (bacteria)
SequenceString: MSFHITPTAA ARDSETKQID HNDSIRASYM TIEELHDAGA ALSRDGADSL PGFMEFDFFE RHRENEKEIL RVYRTTAVDA ENGATITPA AEWLLDNHYV IEEAIQEVRR DFPRKFYRQL PTMTVGGVTI PRVMALGWLY VAHTHSTVSR ENMTALVDGY Q TSQTLQIG ...String:
MSFHITPTAA ARDSETKQID HNDSIRASYM TIEELHDAGA ALSRDGADSL PGFMEFDFFE RHRENEKEIL RVYRTTAVDA ENGATITPA AEWLLDNHYV IEEAIQEVRR DFPRKFYRQL PTMTVGGVTI PRVMALGWLY VAHTHSTVSR ENMTALVDGY Q TSQTLQIG ELWALPSIIR FVLIENLRRI SIRVERSRRM RQKANEVVDE IIRLNDAEAS AALLKQVDSL VDDPTFATQF LY RLRNGSQ TSGFAVAWLE ERLHAAGTDA ENVMMSEHNR LASGNVTMGN IVKSLREIDD TEWSVWFEEV SHIDKVLREE TDY EILDFG SRNTYRNTIE LLARRSPRTE VEVARAAVEM ARSDLPAGAD ENHRVNVGSV LVGQRRFELE KALGYRPLAS QHIV RSMRK FNWLAIAAPV LLITAVAMLA VGWFLAKAGM PWYVVTAFLL MFALPASEGA TGLFNTLVTF FVKPFRLVGY EFKNG IPED ARTLVAVPCM LTSRDSVDEM MRNIEVHYLA NPHGEIYFSL VSDWRDAPYE QSDEDLEILD YAKRELAALN SRYAFD GKT RFYLLHRRRI YNSAEECWMG WERKRGKLHE LNMLLRGDKD TTFLGGSNIV PADVKYVMTL DADTRLMRDA VTKLVGK MH HPINRPKIDP VSGRVVEGYG LLQPRVTPSL TTGKDASVFQ RVFSINRGID PYVFTVSDVY QDLTSEGTFT GKGLYDVD A FEAALKGRIE ENSILSHDLL EGSFARCALV TDVELVEDFP TRYEVEVSRQ HRWARGDWQL LPFIIDRARG VTAIGRWKM VDNLRRSLTP IAWFFASILG WYFMDPLGAL IWQILLIFSL FVAPTLSLLS GLVPRSTDIV PQAHFFTIWS EIRATNAQVA LRIVFIADA ACMMTDAIVR SLYRLLVSHK LMLEWRTAAS MQSSAQGSIV DYYRQMWHAP VVAMLGLLFA ALPGDNAFLI G IPFTLLWV LSPAVAWYVS QSAETEDRLF VSEHVSFELR KIARRTWRYY EAFVTPQENH LPPDNFQETP EPIVASRTSP TN IGVYLLS VISARQFGWI SFADTLERIE NTIQTVEKME KHRGHLYNWY HTDTLQTLGP RYVSAVDSGN LAGHLIAVSS ACR DWAEAP SAHLQGNLDG IGDVAGILRE TLKALPDNRK TLRPLHRRLE ERIIGFSNAL ASVKREHEFA SIRVINLAVL ARDI QKLAT NVDHEVKSAQ SAEVTRWAQL LVESCEAHIS DSAIDLTNME PLRQRLASLR DRSRNLAFSM DFTFLYRKDR RLLSI GYRV ESKELDEACY DLLASECRLT SLFAIAKGDL PTEHWYRLGR QVVPIGAQGA LVSWSGSMFE YLMPPLVMQE RQGGIL NQT NNLIVKEQMN HGRRLGTPWG ISEAAFNARD HNMNYQYTNF GVPTLGLKRG LGQNAVIAPY ASILASQYDP DGALENL DK LRKLGALGQY GFHDAVDFTP TRVPDGKVCA VVYNYYAHHH GMSIAAVANV AFDGVLRELF HSDPVIEAAE LLLQEKAP R EVPVMSAKYE PETPGKEQAD LLRAEVRSIA DPAVRDREVV FLSNGHYSTM LTSTGAGYSK WNGQAISRWK ADPTDDRWG TFIFLRDTTN GQWWSATAEP RVIEGEKTKT IFTDDKAEFH KTIGDLQSVV ECIVATEHDA EGRRITLLNV GSEDRYIEVT SYMEPVIAS EDDDNAHPLF SRMFVQTEIG RRGDVIRAWR NRRSQNEPGT VIAHLAADNA GPSRPTEFET DRAKFIGRGR S LREAAAFD AGATLSSSDG FTLDPILSLR RTVRVPAGKK VSVIFWTIAA PSREEVDKAI DRYRHPDAFA HELVHAWTRT QV QMRHVGV TSQQAAAFQH LGRYLTYPDM HLRADSETLK TGLASQRALW PLAISGDFPI FSLRINDDMD MDIAREALSA HEY LRSRGV IFDLVIVNER AASYAQDMQH ALDHISETQR RINPADGGRP HVFSVRRDLM DEETWSALLA ASRVVLHVRN GKIV DQINR AVSLFAANRG PDGSSDAAQA RLPVPAFPVA EPVEDAGDLD FWNGFGGFAK NGQEYVVRLN GGQSTPHPWI NVISN ENFG FHISAEGAGF SWSRNSRDYQ LTPWTNDPVI NRPGEAFYVA DVETGKLYTP CAALSRDPEA MFETRHGLGY SILTGV ADT LEVELTQTVD REKPVKFSQV IVRNKGSKSR RLKVYAYVEW VLGNNGQKSA PFILSRHDAG SNAIFASNPY SIDYSAR TS FLTLDSEASG FTTSRREFIG RFGSAQAPQG IVAGAALSGT TEVDGDPCAA LMQEIHLKPG EERHMTFILG DADNAEEA E ALVKDVRQAD FLSVLEESKK FWTGFTGQLQ VSTPDAGFNH MVNNWLPYQA LACRILARTA FYQSSGAFGF RDQLQDTLA FLLYQPDLAR TQILRAAGRQ FPEGDVQHWW LPLTGAGVRT TISDDVVWLA YAINQYVSAT GDAAILDESI PFLKGPALMP GQHDAFFQP ETSERSATLY EHAALALDLA IHRTGENGLP LILGGDWNDG MNRVGVGGKG TSVWLGWFLA GALRDFIEIA E KRGDTDRV GKWASHREKL RHVLETAGWD GSYYRRGYFD DGTPLGSASS EECQIDSLGQ SWSVLSGEGE EGRSRQAMDA VM EHLVDEK TGIIRLFTPP FSRASHDPGY IKGYPPGVRE NGGQYTHAAT WVVLALAKQG RAQEAWNCFK LLNPVNHALD AAS SETYRV EPYVVTADVY GEGAYAGRGG WSWYTGSAGW LYRAAVEGIL GITRTDGKLH VSPSLPEDWS GFSIRITLDG KARD IAVSR KAGTADVSVS VDG

UniProtKB: Cyclic beta-(1,2)-glucan synthase NdvB

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Macromolecule #4: URIDINE-5'-DIPHOSPHATE-GLUCOSE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE-GLUCOSE / type: ligand / ID: 4 / Number of copies: 1 / Formula: UPG
Molecular weightTheoretical: 566.302 Da
Chemical component information

ChemComp-UPG:
URIDINE-5'-DIPHOSPHATE-GLUCOSE

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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