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- EMDB-70290: N. brasiliensis GlfT2 in a styrene maleic acid liponanoparticle (... -

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Basic information

Entry
Database: EMDB / ID: EMD-70290
TitleN. brasiliensis GlfT2 in a styrene maleic acid liponanoparticle (C1 Unmasked Map)
Map data
Sample
  • Complex: Tetrameric complex of GlfT2
    • Protein or peptide: Galactofuranosyl Transferase 2
KeywordsGlycosyltransferase / Monotopic / SMALP / Tetramer / Galactofuranose / TRANSFERASE
Function / homologyGalactofuranosyltransferase GlfT2, N-terminal / Galactofuranosyltransferase-2, C-terminal / Galactofuranosyltransferase 2 N-terminal / Galactofuranosyltransferase-2, domain 3 / Glycosyltransferase like family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / Galactofuranosyltransferase
Function and homology information
Biological speciesNocardia brasiliensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsCarter AW / Dodge GJ / Kiessling LL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01 AI126592-10 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM148069 United States
CitationJournal: To Be Published
Title: Structural Insights into Sequence-Controlled Polymerization by the Monotopic Glycosyltransferase GlfT2
Authors: Carter AW / Keys AM / Dodge GJ / Justen AM / Taylor KI / Imperiali B / Drennan CL / Kulik HJ / Kiessling LL
History
DepositionApr 22, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70290.png

Downloads & links

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Map

FileDownload / File: emd_70290.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.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.1380457 - 0.30889672
Average (Standard dev.)0.000008650942 (±0.0084320735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70290_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70290_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70290_half_map_2.map
Projections & Slices
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Sample components

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Entire : Tetrameric complex of GlfT2

EntireName: Tetrameric complex of GlfT2
Components
  • Complex: Tetrameric complex of GlfT2
    • Protein or peptide: Galactofuranosyl Transferase 2

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Supramolecule #1: Tetrameric complex of GlfT2

SupramoleculeName: Tetrameric complex of GlfT2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nocardia brasiliensis (bacteria)
Molecular weightTheoretical: 295 KDa

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Macromolecule #1: Galactofuranosyl Transferase 2

MacromoleculeName: Galactofuranosyl Transferase 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
EC number: galactofuranosylgalactofuranosylrhamnosyl-N-acetylglucosaminyl-diphospho-decaprenol beta-1,5/1,6-galactofuranosyltransferase
Source (natural)Organism: Nocardia brasiliensis (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSWSHPQF EKSSGLVPRG SHMTSQSLLD DMATETRAKS LLQRIILPRP GEPLDVRTLY VEESATNARR AHAATRTSLS IGAESEVSFC TYFNALPASY WRRWSILSAV VLRLELAGHG RVDVYRSKAD GSRIHVQGKE FAVAPGTESV SVEFETDLGP FEDGGWIWFD ...String:
MGSSWSHPQF EKSSGLVPRG SHMTSQSLLD DMATETRAKS LLQRIILPRP GEPLDVRTLY VEESATNARR AHAATRTSLS IGAESEVSFC TYFNALPASY WRRWSILSAV VLRLELAGHG RVDVYRSKAD GSRIHVQGKE FAVAPGTESV SVEFETDLGP FEDGGWIWFD ITSDTAVTLL AGGWYAPIEA PGAGTIACGM PTFNRPTDLV KTLGALGSDP LVLGQVAAVI VADQGNRKVV DEPGFDEAAA VLGDRLVIRD QPNLGGSGGY SRVMYEALKN TDAEYIVYMD DDIEIEPDSI LRALAFARFA KSPMLVGGQM LNLQERSHLH SMGEVVDRGI FMWTSAPNVE YDHDFAKHPL KDRDNSKLLH RRIDVDFNGW WTCVIPRQVA EQIGQPLPLF LKWDDVEYGL RARDHGYPTV TLPGAAVWHM AWSDKDDAID WQAYFHLRNR LVVASLHLPG NGKAMVVNTI KATLKHLLCL EYSTVAIQNL AIRDYLAGPE RLFQLLPSAL GAVHALRKQY PDAVILPSST ELPLASHLEV GAVAEPANPI AKVVRLAKGV LHNLRPAHAR HHETPQLNVP TLDARWFLLS QVDGVTVTTA DGRGVVYRKR DPRQALGLFK EAMRLRKELA ARFPEMQQRY RAAHPQLTST AAWENAFGLG AQTKGEKS

UniProtKB: Galactofuranosyltransferase

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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

Concentration1.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
100.0 mMHEPES
150.0 mMsodium chlorideNaCl
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 3.43 sec. / Average electron dose: 50.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1552517
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 182122
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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