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- EMDB-33423: structure of a membrane-integrated glycosyltransferase -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33423
Titlestructure of a membrane-integrated glycosyltransferase
Map data
Sample
  • Complex: membrane-integrated glycosyltransferase
    • Protein or peptide: Chitin synthase 1
  • Ligand: TETRADECANE
  • Ligand: DODECANE
  • Ligand: HEPTANE
  • Ligand: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate
Keywordsmembrane protein / glycosyltransferase / TRANSFERASE
Function / homology
Function and homology information


chitosome / chitin synthase / chitin synthase activity / chitin biosynthetic process / 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-like glycosyltransferase domain / Chitin synthase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWu YN / Zhang M / Yang YZ / Ding XY / Liu XT / Zhang MJ / Yu HJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2022
Title: Structures and mechanism of chitin synthase and its inhibition by antifungal drug Nikkomycin Z.
Authors: Yanan Wu / Min Zhang / Yizheng Yang / Xuyang Ding / Ping Yang / Kai Huang / Xinlin Hu / Mingjie Zhang / Xiaotian Liu / Hongjun Yu /
History
DepositionMay 13, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33423.png

Downloads & links

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Map

FileDownload / File: emd_33423.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 304 pix.
= 279.68 Å		0.92 Å/pix.
x 304 pix.
= 279.68 Å		0.92 Å/pix.
x 304 pix.
= 279.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05634144 - 0.11093479
Average (Standard dev.)0.000015033079 (±0.003266719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 279.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33423_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33423_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : membrane-integrated glycosyltransferase

EntireName: membrane-integrated glycosyltransferase
Components
  • Complex: membrane-integrated glycosyltransferase
    • Protein or peptide: Chitin synthase 1
  • Ligand: TETRADECANE
  • Ligand: DODECANE
  • Ligand: HEPTANE
  • Ligand: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate

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Supramolecule #1: membrane-integrated glycosyltransferase

SupramoleculeName: membrane-integrated glycosyltransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Chitin synthase 1

MacromoleculeName: Chitin synthase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: chitin synthase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 130.001141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSDQNNRSRN EYHSNRKNEP SYELQNAHSG LFHSSNEELT NRNQRYTNQN ASMGSFTPVQ SLQFPEQSQQ TNMLYNGDDG NNNTINDNE RDIYGGFVNH HRQRPPPATA EYNDVFNTNS QQLPSEHQYN NVPSYPLPSI NVIQTTPELI HNGSQTMATP I ERPFFNEN ...String:
MSDQNNRSRN EYHSNRKNEP SYELQNAHSG LFHSSNEELT NRNQRYTNQN ASMGSFTPVQ SLQFPEQSQQ TNMLYNGDDG NNNTINDNE RDIYGGFVNH HRQRPPPATA EYNDVFNTNS QQLPSEHQYN NVPSYPLPSI NVIQTTPELI HNGSQTMATP I ERPFFNEN DYYYNNRNSR TSPSIASSSD GYADQEARPI LEQPNNNMNS GNIPQYHDQP FGYNNGYHGL QAKDYYDDPE GG YIDQRGD DYQINSYLGR NGEMVDPYDY ENSLRHMTPM ERREYLHDDS RPVNDGKEEL DSVKSGYSHR DLGEYDKDDF SRD DEYDDL NTIDKLQFQA NGVPASSSVS SIGSKESDII VSNDNLTANR ALKRSGTEIR KFKLWNGNFV FDSPISKTLL DQYA TTTEN ANTLPNEFKF MRYQAVTCEP NQLAEKNFTV RQLKYLTPRE TELMLVVTMY NEDHILLGRT LKGIMDNVKY MVKKK NSST WGPDAWKKIV VCIISDGRSK INERSLALLS SLGCYQDGFA KDEINEKKVA MHVYEHTTMI NITNISESEV SLECNQ GTV PIQLLFCLKE QNQKKINSHR WAFEGFAELL RPNIVTLLDA GTMPGKDSIY QLWREFRNPN VGGACGEIRT DLGKRFV KL LNPLVASQNF EYKMSNILDK TTESNFGFIT VLPGAFSAYR FEAVRGQPLQ KYFYGEIMEN EGFHFFSSNM YLAEDRIL C FEVVTKKNCN WILKYCRSSY ASTDVPERVP EFILQRRRWL NGSFFASVYS FCHFYRVWSS GHNIGRKLLL TVEFFYLFF NTLISWFSLS SFFLVFRILT VSIALAYHSA FNVLSVIFLW LYGICTLSTF ILSLGNKPKS TEKFYVLTCV IFAVMMIYMI FCSIFMSVK SFQNILKNDT ISFEGLITTE AFRDIVISLG STYCLYLISS IIYLQPWHML TSFIQYILLS PSYINVLNIY A FCNVHDLS WGTKGAMANP LGKINTTEDG TFKMEVLVSS SEIQANYDKY LKVLNDFDPK SESRPTEPSY DEKKTGYYAN VR SLVIIFW VITNFIIVAV VLETGGIADY IAMKSISTDD TLETAKKAEI PLMTSKASIY FNVILWLVAL SALIRFIGCS IYM IVRFFK KVTFR

UniProtKB: Chitin synthase 1

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Macromolecule #2: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 2 / Number of copies: 16 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #3: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 3 / Number of copies: 10 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #4: HEPTANE

MacromoleculeName: HEPTANE / type: ligand / ID: 4 / Number of copies: 14 / Formula: HP6
Molecular weightTheoretical: 100.202 Da
Chemical component information

ChemComp-HP6:
HEPTANE

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Macromolecule #5: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22l...

MacromoleculeName: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate
type: ligand / ID: 5 / Number of copies: 2 / Formula: 0V9
Molecular weightTheoretical: 689.943 Da
Chemical component information

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

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93641
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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