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- PDB-9nyk: Cryo-EM structure of the glycosyltransferase GtrB in the pre-inte... -

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Basic information

Entry
Database: PDB / ID: 9nyk
TitleCryo-EM structure of the glycosyltransferase GtrB in the pre-intermediate state
ComponentsGlycosyltransferase sll0501
KeywordsMEMBRANE PROTEIN / glycosyltransferase / polyisoprenyl
Function / homology
Function and homology information


Transferases; Glycosyltransferases / glycosyltransferase activity / plasma membrane
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Chem-5TR / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Uncharacterized glycosyltransferase sll0501
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsMorgan, R.T. / Motta, S. / Gil-Iturbe, E. / di Muccio, G. / Bhattacharjee, B. / Romagnoli, A. / Anwar, M.T. / Mishra, B. / Ashraf, K. / Bang, I. ...Morgan, R.T. / Motta, S. / Gil-Iturbe, E. / di Muccio, G. / Bhattacharjee, B. / Romagnoli, A. / Anwar, M.T. / Mishra, B. / Ashraf, K. / Bang, I. / di Marino, D. / Lowary, T.L. / Quick, M. / Petrou, V.I. / Stowell, M.H.B. / Nygaard, R. / Mancia, F.
Funding support United States, 5items
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: Morgan, R.T. / Motta, S. / Gil-Iturbe, E. / Bhattacharjee, B. / Anwar, M.T. / Di Muccio, G. / Romagnoli, A. / Mishra, B. / Ashraf, K.U. / Bang, I. / Di Marino, D. / Lowary, T.L. / Quick, M. ...Authors: Morgan, R.T. / Motta, S. / Gil-Iturbe, E. / Bhattacharjee, B. / Anwar, M.T. / Di Muccio, G. / Romagnoli, A. / Mishra, B. / Ashraf, K.U. / Bang, I. / Di Marino, D. / Lowary, T.L. / Quick, M. / Petrou, V.I. / Stowell, M.H.B. / Nygaard, R. / Mancia, F.
History
DepositionMar 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase sll0501
B: Glycosyltransferase sll0501
C: Glycosyltransferase sll0501
D: Glycosyltransferase sll0501
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,02916
Polymers157,2784
Non-polymers5,75212
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Glycosyltransferase sll0501


Mass: 39319.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Gene: sll0501
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q55487, Transferases; Glycosyltransferases
#2: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
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 / Undecaprenyl phosphate


Mass: 847.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H91O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GtrB in the pre-intermediate state / Type: COMPLEX / Details: Bound to Undecaprenyl phosphate and UDP-glucose / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.146673 MDa / Experimental value: NO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1.22 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Vitrification carried out under UV exposure for 17 ms

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 58.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9219

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44598 / Symmetry type: POINT
RefinementHighest resolution: 2.98 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00510648
ELECTRON MICROSCOPYf_angle_d0.61114460
ELECTRON MICROSCOPYf_dihedral_angle_d7.3051448
ELECTRON MICROSCOPYf_chiral_restr0.0411624
ELECTRON MICROSCOPYf_plane_restr0.0071772

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