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- EMDB-70273: N. brasiliensis GlfT2 in a styrene maleic acid liponanoparticle -

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Basic information

Entry
Database: EMDB / ID: EMD-70273
TitleN. brasiliensis GlfT2 in a styrene maleic acid liponanoparticle
Map data
Sample
  • Complex: Homotetrameric Complex of Galactofuranosyltransferase 2
    • Protein or peptide: Galactofuranosyltransferase
  • Ligand: MAGNESIUM ION
KeywordsGlycosyltransferase / Membrane / Galactofuranose / Galactan / TRANSFERASE / SMALP
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: 3.02 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 AI126592-09 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F31 GM148069 United States
CitationJournal: To Be Published
Title: Structural Insights into Sequence-Controlled Polymerization by the Monotopic Glycosyltransferase GlfT2
Authors: Carter AW / Dodge GJ / Keys AM / Justen AM / Taylor KI / Imperiali B / Kulik HJ / Kiessling LL
History
DepositionApr 19, 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_70273.png

Downloads & links

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Map

FileDownload / File: emd_70273.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesX (Sec.)Y (Row.)Z (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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-26.770109999999999 - 47.097476999999998
Average (Standard dev.)0.000000000001789 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_70273_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_70273_additional_1.map
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Half map: #1

Fileemd_70273_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #2

Fileemd_70273_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Homotetrameric Complex of Galactofuranosyltransferase 2

EntireName: Homotetrameric Complex of Galactofuranosyltransferase 2
Components
  • Complex: Homotetrameric Complex of Galactofuranosyltransferase 2
    • Protein or peptide: Galactofuranosyltransferase
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Homotetrameric Complex of Galactofuranosyltransferase 2

SupramoleculeName: Homotetrameric Complex of Galactofuranosyltransferase 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nocardia brasiliensis (bacteria)
Molecular weightTheoretical: 295 KDa

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Macromolecule #1: Galactofuranosyltransferase

MacromoleculeName: Galactofuranosyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nocardia brasiliensis (bacteria)
Molecular weightTheoretical: 73.853906 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSWSHPQF EKSSGLVPRG SHMTSQSLLD DMATETRAKS LLQRIILPRP GEPLDVRTLY VEESATNARR AHAATRTSLS IGAESEVSF CTYFNALPAS YWRRWSILSA VVLRLELAGH GRVDVYRSKA DGSRIHVQGK EFAVAPGTES VSVEFETDLG P FEDGGWIW ...String:
MGSSWSHPQF EKSSGLVPRG SHMTSQSLLD DMATETRAKS LLQRIILPRP GEPLDVRTLY VEESATNARR AHAATRTSLS IGAESEVSF CTYFNALPAS YWRRWSILSA VVLRLELAGH GRVDVYRSKA DGSRIHVQGK EFAVAPGTES VSVEFETDLG P FEDGGWIW FDITSDTAVT LLAGGWYAPI EAPGAGTIAC GMPTFNRPTD LVKTLGALGS DPLVLGQVAA VIVADQGNRK VV DEPGFDE AAAVLGDRLV IRDQPNLGGS GGYSRVMYEA LKNTDAEYIV YMDDDIEIEP DSILRALAFA RFAKSPMLVG GQM LNLQER SHLHSMGEVV DRGIFMWTSA PNVEYDHDFA KHPLKDRDNS KLLHRRIDVD FNGWWTCVIP RQVAEQIGQP LPLF LKWDD VEYGLRARDH GYPTVTLPGA AVWHMAWSDK DDAIDWQAYF HLRNRLVVAS LHLPGNGKAM VVNTIKATLK HLLCL EYST VAIQNLAIRD YLAGPERLFQ LLPSALGAVH ALRKQYPDAV ILPSSTELPL ASHLEVGAVA EPANPIAKVV RLAKGV LHN LRPAHARHHE TPQLNVPTLD ARWFLLSQVD GVTVTTADGR GVVYRKRDPR QALGLFKEAM RLRKELAARF PEMQQRY RA AHPQLTSTAA WENAFGLGAQ TKGEKS

UniProtKB: Galactofuranosyltransferase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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:
ConcentrationName
100.0 mMHEPES
150.0 mMsodium chloride
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 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 reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.02 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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Atomic model buiding 1

Initial modelPDB ID:

9dtp


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9oa3:
N. brasiliensis GlfT2 in a styrene maleic acid liponanoparticle

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