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- EMDB-49935: Cryo-EM structure of the glycosyltransferase GtrB in the pre-inte... -

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Entry
Database: EMDB / ID: EMD-49935
TitleCryo-EM structure of the glycosyltransferase GtrB in the pre-intermediate state
Map datastructure of the glycosyltransferase GtrB in the pre-intermediate state
Sample
  • Complex: GtrB in the pre-intermediate state
    • Protein or peptide: Glycosyltransferase sll0501
  • Ligand: URIDINE-5'-DIPHOSPHATE-GLUCOSE
  • Ligand: [(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl] dihydrogen phosphate
  • Ligand: MAGNESIUM ION
Keywordsglycosyltransferase / polyisoprenyl / MEMBRANE PROTEIN
Function / homologyTransferases; Glycosyltransferases / : / Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / plasma membrane / Uncharacterized glycosyltransferase sll0501
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsMorgan RT / Motta S / Gil-Iturbe E / di Muccio G / Bhattacharjee B / Romagnoli A / Anwar MT / Mishra B / Ashraf K / Bang I ...Morgan RT / Motta S / Gil-Iturbe E / di Muccio G / Bhattacharjee B / Romagnoli A / Anwar MT / Mishra B / Ashraf K / Bang I / di Marino D / Lowary TL / Quick M / Petrou VI / Stowell MHB / Nygaard R / Mancia F
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM132120 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS120496 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM123228 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM123228 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150831 United States
CitationJournal: Nat Commun / Year: 2025
Title: Mechanistic snapshots of lipid-linked sugar transfer.
Authors: Ryan T Morgan / Stefano Motta / Eva Gil-Iturbe / Biddut Bhattacharjee / Mohammad T Anwar / Giovanni Di Muccio / Alice Romagnoli / Bedangshu Mishra / Khuram U Ashraf / Injin Bang / Daniele Di ...Authors: Ryan T Morgan / Stefano Motta / Eva Gil-Iturbe / Biddut Bhattacharjee / Mohammad T Anwar / Giovanni Di Muccio / Alice Romagnoli / Bedangshu Mishra / Khuram U Ashraf / Injin Bang / Daniele Di Marino / Todd L Lowary / Matthias Quick / Vasileios I Petrou / Michael H B Stowell / Rie Nygaard / Filippo Mancia /
Abstract: Enzymes undergo dynamic conformational changes during catalysis, yet conventional high-resolution structural methods typically capture only the most stable states. Here, we address this gap using ...Enzymes undergo dynamic conformational changes during catalysis, yet conventional high-resolution structural methods typically capture only the most stable states. Here, we address this gap using rapid UV photolysis of a chemically caged substrate with cryogenic time-resolved electron microscopy (cryo-TREM). We elucidate the catalytic mechanism of GtrB, a membrane-bound glycosyltransferase that transfers glucose from UDP-glucose to the lipid carrier undecaprenyl phosphate. We visualized how GtrB, which has an active site ~15 Å from the membrane, transitions during the catalytic cycle to move each substrate in proximity for catalysis. From a single dataset, we resolved distinct conformational states: the initial substrate-bound state, a catalytically poised intermediate, and the product-bound state. Through molecular dynamics simulations and biochemical analyses, we identify coordinated movements within the active site that drive catalysis. These findings provide a molecular framework for understanding how glycosyltransferases function and highlight a broadly applicable strategy for capturing dynamic enzymatic states in native-like environments.
History
DepositionMar 27, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49935.png

Downloads & links

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Map

FileDownload / File: emd_49935.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of the glycosyltransferase GtrB in the pre-intermediate state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.135
Minimum - Maximum-0.8229858 - 1.1736498
Average (Standard dev.)0.0022616363 (±0.05164329)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49935_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49935_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49935_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GtrB in the pre-intermediate state

EntireName: GtrB in the pre-intermediate state
Components
  • Complex: GtrB in the pre-intermediate state
    • Protein or peptide: Glycosyltransferase sll0501
  • Ligand: URIDINE-5'-DIPHOSPHATE-GLUCOSE
  • Ligand: [(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl] dihydrogen phosphate
  • Ligand: MAGNESIUM ION

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Supramolecule #1: GtrB in the pre-intermediate state

SupramoleculeName: GtrB in the pre-intermediate state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Bound to Undecaprenyl phosphate and UDP-glucose
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Molecular weightTheoretical: 146.673 KDa

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Macromolecule #1: Glycosyltransferase sll0501

MacromoleculeName: Glycosyltransferase sll0501 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: Transferases; Glycosyltransferases
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Molecular weightTheoretical: 39.31943 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MHHHHHHSSG VDLGTENLYF QSNATIELSI VIPMYNEEDN LEHLFARLLE VLTPLKITYE IICVNDGSKD KTLKQLIDCY QSNRQIKIV NLSRNFGKEI ALSAGIDYAQ GNAVIPIDAD LQDPPELIHE LVDKWREGYD IVYATRRSRQ GETWVKQFTA K MFYKVIGR ...String:
MHHHHHHSSG VDLGTENLYF QSNATIELSI VIPMYNEEDN LEHLFARLLE VLTPLKITYE IICVNDGSKD KTLKQLIDCY QSNRQIKIV NLSRNFGKEI ALSAGIDYAQ GNAVIPIDAD LQDPPELIHE LVDKWREGYD IVYATRRSRQ GETWVKQFTA K MFYKVIGR MTEIKIPPNT GDFRLMDRKV VNAIKQLPER TRFMKGLFAW VGYRQTFVLF DREPRFQGQT KWNYWKLWNF AL DGIFSFS LLPLKVWTYL GSIISLLSLA YASFLILKTI TLGVDVPGYA SLMVAILFLG GVQLISLGVI GEYLGRVYEE VKA RPLYLV SDLWGLEYLP LEKLN

UniProtKB: Uncharacterized glycosyltransferase sll0501

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Macromolecule #2: URIDINE-5'-DIPHOSPHATE-GLUCOSE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE-GLUCOSE / type: ligand / ID: 2 / Number of copies: 4 / Formula: UPG
Molecular weightTheoretical: 566.302 Da
Chemical component information

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

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Macromolecule #3: [(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38...

MacromoleculeName: [(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl] dihydrogen phosphate
type: ligand / ID: 3 / Number of copies: 4 / Formula: 5TR
Molecular weightTheoretical: 847.282 Da
Chemical component information

ChemComp-5TR:
[(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl] dihydrogen phosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / 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

Concentration1.22 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification carried out under UV exposure for 17 ms.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9219 / Average exposure time: 2.5 sec. / Average electron dose: 58.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ekp

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44598
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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