7ZLI | pdb_00007zli

Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bound to CMT2-Fab and anti-Fab nanobody

• PDB DOI: https://doi.org/10.2210/pdb7ZLI/pdb
• EM Map EMD-14781: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): synthetic construct, Caenorhabditis elegans
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2022-04-15 Released: 2023-01-11 
• Deposition Author(s): Bloch, J.S., Mukherjee, S., Boilevin, J., Irobalieva, R., Darbre, T., Reymond, J.L., Kossiakoff, A.A., Goddard-Borger, E.D., Locher, K.P.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase.

Bloch, J.S., John, A., Mao, R., Mukherjee, S., Boilevin, J., Irobalieva, R.N., Darbre, T., Scott, N.E., Reymond, J.L., Kossiakoff, A.A., Goddard-Borger, E.D., Locher, K.P.

(2023) Nat Chem Biol 19: 575-584

• PubMed: 36604564 
• DOI: https://doi.org/10.1038/s41589-022-01219-9
• Primary Citation Related Structures: 
  7ZLG, 7ZLH, 7ZLI, 7ZLJ


• PubMed 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-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.

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Organizational Affiliation: 
• Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
Laboratory of Molecular Neurobiology and Biophysics and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. [e-mail].
Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia. [e-mail].
Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 143.13 kDa 
• Atom Count: 9,582 
• Modeled Residue Count: 1,218 
• Deposited Residue Count: 1,281 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CMT2-Fab heavy chain	A [auth H]	236	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-Fab nanobody	B [auth K]	123	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CMT2-Fab light chain	C [auth L]	215	synthetic construct	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q7Z3Y4 (Homo sapiens) Explore Q7Z3Y4  Go to UniProtKB:  Q7Z3Y4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
C-mannosyltransferase dpy-19	D [auth A]	707	Caenorhabditis elegans	Mutation(s): 0  Gene Names: dpy-19, F22B7.10 EC: 2.4.1 Membrane Entity: Yes
UniProt
Find proteins for P34413 (Caenorhabditis elegans) Explore P34413  Go to UniProtKB:  P34413

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IZY (Subject of Investigation/LOI)	E [auth A]	Dolichol monophosphate beta-D-Mannose C31 H55 O9 P AGLXCEGQRIYVRV-YNCWARPRSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Bloch, J.S., Mukherjee, S., Boilevin, J., Irobalieva, R., Darbre, T., Reymond, J.L., Kossiakoff, A.A., Goddard-Borger, E.D., Locher, K.P.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 1.1: 2023-01-18
  Changes: Database references
• Version 1.2: 2023-05-10
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.4: 2025-07-02
  Changes: Data collection
• Version 1.5: 2025-07-30
  Changes: Data collection, Derived calculations, Structure summary