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- PDB-7xs6: structure of a membrane-integrated glycosyltransferase with inhibitor -

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Basic information

Entry
Database: PDB / ID: 7xs6
Titlestructure of a membrane-integrated glycosyltransferase with inhibitor
ComponentsChitin synthase 1
KeywordsMEMBRANE PROTEIN / glycosyltransferase / TRANSFERASE
Function / homology
Function and homology information


chitosome / chitin synthase / chitin synthase activity / : / septum digestion after cytokinesis / cell septum / cell periphery / cell wall organization / plasma membrane
Similarity search - Function
Chitin synthase N-terminal / Chitin synthase N-terminal / Fungal chitin synthase / Chitin synthase / Chitin synthase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Chem-0V9 / Chem-BGI / TETRADECANE / DODECANE / HEPTANE / Chitin synthase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWu, Y.N. / Zhang, M. / Yang, Y.Z. / Ding, X.Y. / Liu, X.T. / Zhang, M.J. / Yu, H.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: structure of a membrane-integrated glycosyltransferase with inhibitor
Authors: Wu, Y.N. / Zhang, M. / Yang, Y.Z. / Ding, X.Y. / Liu, X.T. / Zhang, M.J. / Yu, H.J.
History
DepositionMay 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Chitin synthase 1
A: Chitin synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,65346
Polymers260,0022
Non-polymers8,65144
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Chitin synthase 1 / Chitin-UDP acetyl-glucosaminyl transferase 1


Mass: 130001.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CHS1, YNL192W, N1404 / Production host: Homo sapiens (human) / References: UniProt: P08004, chitin synthase

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Non-polymers , 5 types, 44 molecules

#2: Chemical
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C14H30
#3: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical
ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C7H16
#5: Chemical ChemComp-BGI / (2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name) / Nikkomycin Z


Mass: 495.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N5O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antifungal*YM
#6: Chemical ChemComp-0V9 / (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate


Mass: 689.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H72NO8P

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Details

Has ligand of interestY

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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: membrane-integrated glycosyltransferase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188337 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00512696
ELECTRON MICROSCOPYf_angle_d0.61416992
ELECTRON MICROSCOPYf_dihedral_angle_d8.3782006
ELECTRON MICROSCOPYf_chiral_restr0.0441866
ELECTRON MICROSCOPYf_plane_restr0.0052036

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