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Yorodumi- PDB-7zlj: Cryo-EM structure of C-mannosyltransferase CeDPY19, in ternary co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zlj | ||||||
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Title | Cryo-EM structure of C-mannosyltransferase CeDPY19, in ternary complex with Dol25-P-C-Man and acceptor peptide, bound to CMT2-Fab and anti-Fab nanobody | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / C-mannosyltransferase | ||||||
Function / homology | Function and homology information protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan / mannosyltransferase activity / nuclear inner membrane / Transferases; Glycosyltransferases; Hexosyltransferases / nervous system development / carbohydrate metabolic process / cell differentiation / immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm ...protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan / mannosyltransferase activity / nuclear inner membrane / Transferases; Glycosyltransferases; Hexosyltransferases / nervous system development / carbohydrate metabolic process / cell differentiation / immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | synthetic construct (others) Caenorhabditis elegans (invertebrata) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å | ||||||
Authors | Bloch, J.S. / Mao, R. / Mukherjee, S. / Boilevin, J. / Irobalieva, R. / Darbre, T. / Reymond, J.L. / Kossiakoff, A.A. / Goddard-Borger, E.D. / Locher, K.P. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zlj.cif.gz | 222.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zlj.ent.gz | 178.1 KB | Display | PDB format |
PDBx/mmJSON format | 7zlj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zlj_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7zlj_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7zlj_validation.xml.gz | 55 KB | Display | |
Data in CIF | 7zlj_validation.cif.gz | 78.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/7zlj ftp://data.pdbj.org/pub/pdb/validation_reports/zl/7zlj | HTTPS FTP |
-Related structure data
Related structure data | 14782MC 7zlgC 7zlhC 7zliC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Antibody , 3 types, 3 molecules HKL
#1: Antibody | Mass: 25000.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 13390.644 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#3: Antibody | Mass: 23238.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3Y4 |
-Protein / Protein/peptide , 2 types, 2 molecules AP
#4: Protein | Mass: 80892.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: dpy-19, F22B7.10 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P34413, Transferases; Glycosyltransferases; Hexosyltransferases |
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#5: Protein/peptide | Mass: 821.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Non-polymers , 2 types, 11 molecules
#6: Chemical | ChemComp-IZU / [( |
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#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: C-mannosyltransferase CeDPY19, in ternary complex with Dol25-P-C-Man and acceptor peptide, bound to CMT2-Fab and anti-Fab nanobody Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 800 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57289 / Symmetry type: POINT | ||||||||||||||||||||||||
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