[English] 日本語
Yorodumi
- EMDB-14780: Cryo-EM structure of C-mannosyltransferase CeDPY19, in apo state,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14780
TitleCryo-EM structure of C-mannosyltransferase CeDPY19, in apo state, bound to CMT2-Fab and anti-Fab nanobody
Map data
Sample
  • Complex: C-mannosyltransferase CeDPY19, in apo state, 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: water
KeywordsC-mannosyltransferase / MEMBRANE PROTEIN
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 / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cytoplasm
Similarity search - Function
Dpy-19/Dpy-19-like / : / Q-cell neuroblast polarisation / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
C-mannosyltransferase dpy-19
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsBloch JS / Mukherjee S / Irobalieva R / 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-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14780.png

Downloads & links

-
Map

FileDownload / File: emd_14780.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.046399776 - 0.07822573
Average (Standard dev.)-0.00000508659 (±0.0017948879)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_14780_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_14780_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : C-mannosyltransferase CeDPY19, in apo state, bound to CMT2-Fab an...

EntireName: C-mannosyltransferase CeDPY19, in apo state, bound to CMT2-Fab and anti-Fab nanobody
Components
  • Complex: C-mannosyltransferase CeDPY19, in apo state, 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: water

-
Supramolecule #1: C-mannosyltransferase CeDPY19, in apo state, bound to CMT2-Fab an...

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

-
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

-
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

-
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

-
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

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

-
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

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 384830
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more