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- EMDB-14781: Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-14781
TitleCryo-EM structure of C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bound to CMT2-Fab and anti-Fab nanobody
Map data
Sample
  • Complex: C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bound to CMT2-Fab and anti-Fab nanobody
    • Protein or peptide: CMT2-Fab heavy chain
    • Protein or peptide: Anti-Fab nanobody
    • Protein or peptide: CMT2-Fab light chain
    • Protein or peptide: C-mannosyltransferase dpy-19
  • Ligand: Dolichol monophosphate beta-D-Mannose
  • Ligand: water
KeywordsC-mannosyltransferase / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / mannosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / immunoglobulin complex / nervous system development / carbohydrate metabolic process / adaptive immune response / cell differentiation / endoplasmic reticulum membrane / perinuclear region of cytoplasm ...: / mannosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / immunoglobulin complex / nervous system development / carbohydrate metabolic process / adaptive immune response / cell differentiation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Dpy-19/Dpy-19-like / : / Q-cell neuroblast polarisation / Glycoside hydrolase/deacetylase, beta/alpha-barrel / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...Dpy-19/Dpy-19-like / : / Q-cell neuroblast polarisation / Glycoside hydrolase/deacetylase, beta/alpha-barrel / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
C-mannosyltransferase dpy-19 / Ig-like domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsBloch JS / Mukherjee S / Boilevin J / Irobalieva R / Darbre T / Reymond JL / Kossiakoff AA / Goddard-Borger ED / Locher KP
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Chem Biol / Year: 2023
Title: Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase.
Authors: Joël S Bloch / Alan John / Runyu Mao / Somnath Mukherjee / Jérémy Boilevin / Rossitza N Irobalieva / Tamis Darbre / Nichollas E Scott / Jean-Louis Reymond / Anthony A Kossiakoff / Ethan D ...Authors: Joël S Bloch / Alan John / Runyu Mao / Somnath Mukherjee / Jérémy Boilevin / Rossitza N Irobalieva / Tamis Darbre / Nichollas E Scott / Jean-Louis Reymond / Anthony A Kossiakoff / Ethan D Goddard-Borger / Kaspar P Locher /
Abstract: C-linked glycosylation is essential for the trafficking, folding and function of secretory and transmembrane proteins involved in cellular communication processes. The tryptophan C- ...C-linked glycosylation is essential for the trafficking, folding and function of secretory and transmembrane proteins involved in cellular communication processes. The tryptophan C-mannosyltransferase (CMT) enzymes that install the modification attach a mannose to the first tryptophan of WxxW/C sequons in nascent polypeptide chains by an unknown mechanism. Here, we report cryogenic-electron microscopy structures of Caenorhabditis elegans CMT in four key states: apo, acceptor peptide-bound, donor-substrate analog-bound and as a trapped ternary complex with both peptide and a donor-substrate mimic bound. The structures indicate how the C-mannosylation sequon is recognized by this CMT and its paralogs, and how sequon binding triggers conformational activation of the donor substrate: a process relevant to all glycosyltransferase C superfamily enzymes. Our structural data further indicate that the CMTs adopt an unprecedented electrophilic aromatic substitution mechanism to enable the C-glycosylation of proteins. These results afford opportunities for understanding human disease and therapeutic targeting of specific CMT paralogs.
History
DepositionApr 15, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14781.png

Downloads & links

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Map

FileDownload / File: emd_14781.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 400 pix.
= 264. Å		0.66 Å/pix.
x 400 pix.
= 264. Å		0.66 Å/pix.
x 400 pix.
= 264. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.4657803 - 3.3668907
Average (Standard dev.)0.0010567126 (±0.06415242)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_14781_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_14781_half_map_1.map
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AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14781_half_map_2.map
Projections & Slices
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Sample components

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Entire : C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bo...

EntireName: C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bound to CMT2-Fab and anti-Fab nanobody
Components
  • Complex: C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bound to CMT2-Fab and anti-Fab nanobody
    • Protein or peptide: CMT2-Fab heavy chain
    • Protein or peptide: Anti-Fab nanobody
    • Protein or peptide: CMT2-Fab light chain
    • Protein or peptide: C-mannosyltransferase dpy-19
  • Ligand: Dolichol monophosphate beta-D-Mannose
  • Ligand: water

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Supramolecule #1: C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bo...

SupramoleculeName: C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bound to CMT2-Fab and anti-Fab nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: CMT2-Fab heavy chain

MacromoleculeName: CMT2-Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.000723 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NISSSSIHWV RQAPGKGLEW VASISSSYGY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSSSVYWSW WGYSAFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NISSSSIHWV RQAPGKGLEW VASISSSYGY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSSSVYWSW WGYSAFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHT

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Macromolecule #2: Anti-Fab nanobody

MacromoleculeName: Anti-Fab nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.390644 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSQVQLQESG GGLVQPGGSL RLSCAASGRT ISRYAMSWFR QAPGKEREFV AVARRSGDGA FYADSVQGRF TVSRDDAKNT VYLQMNSLK PEDTAVYYCA IDSDTFYSGS YDYWGQGTQV TVSS

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Macromolecule #3: CMT2-Fab light chain

MacromoleculeName: CMT2-Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.23875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQGASEPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQGASEPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

UniProtKB: Ig-like domain-containing protein

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Macromolecule #4: C-mannosyltransferase dpy-19

MacromoleculeName: C-mannosyltransferase dpy-19 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Glycosyltransferases; Hexosyltransferases
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 80.892602 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAKKPKNSPE KSKYSSDTSS SLYSQTWLAS VVIIGLLVGY INYQHVYTLF ENDKHFSHLA DFEREMAYRT EMGLYYSYYK TIINAPSFL EGVQEITHDT VTEHGHEINT LNRFNLYPEV ILAFLYRPFR AFAKSANWQI ELCWQVNRGE LRPVESCEGI G NPHYFYIT ...String:
MAKKPKNSPE KSKYSSDTSS SLYSQTWLAS VVIIGLLVGY INYQHVYTLF ENDKHFSHLA DFEREMAYRT EMGLYYSYYK TIINAPSFL EGVQEITHDT VTEHGHEINT LNRFNLYPEV ILAFLYRPFR AFAKSANWQI ELCWQVNRGE LRPVESCEGI G NPHYFYIT GVFIVAGTVA SSIFYLGVLV SDSIFGGFLS VLCFAFNHGE ATRVQWTPPL RESFAFPFII GHIAILTFVI KY KKSGHSM ILLLTSMAVP ALLFWQFTQF AFFTQICSIF LAFSLDLIPF STAKTVIHSH IISFLIGFLL LFGNEMMITA LYF PSILAL GMIIYISPLL SNLKFRPAYV LFLAIIFASI TLGLKIGLSK GLGIEDDAHI FDILRSKFTS FANFHTRLYT CSAE FDFIQ YSTIEKLCGT LLIPLALISL VTFVFNFVKN TNLLWRNSEE IGENGEILYN VVQLCCSTVM AFLIMRLKLF MTPHL CIVA ALFANSKLLG GDRISKTIRV SALVGVIAIL FYRGIPNIRQ QLNVKGEYSN PDQEMLFDWI QHNTKQDAVF AGTMPV MAN VKLTTLRPIV NHPHYEHVGI RERTLKVYSM FSKKPIAEVH KIMKEMGVNY FVFQLMNCSN DERRPECVYR GMWDEED PK NSGRTALCDL WILAANSKDN SRIAPFKIVY NANRNYIVLK ILEDYKDHDG DYKDHDIDYK DDDDK

UniProtKB: C-mannosyltransferase dpy-19

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Macromolecule #5: Dolichol monophosphate beta-D-Mannose

MacromoleculeName: Dolichol monophosphate beta-D-Mannose / type: ligand / ID: 5 / Number of copies: 1 / Formula: IZY
Molecular weightTheoretical: 602.737 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 13 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.6 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 301020
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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