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

Electron Microscopy
2.99Å resolution
PDB entry 7zli coloured by chain, front view.
PDB entry 7zli coloured by chain, side view.
PDB entry 7zli coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetramer (preferred)
Entry contents: 4 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero tetramer
Accessible surface area: 53481.84 Å2
Buried surface area: 5771.99 Å2
Dissociation area: 1,302.4 Å2
Dissociation energy (ΔGdiss): -7.33 kcal/mol
Dissociation entropy (TΔSdiss): 26.5 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-225601

Macromolecules

CMT2-Fab heavy chain
Chain: H
Length: 236 amino acids
Theoretical weight: 25 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
InterPro:
CMT2-Fab heavy chain in PDB entry 7zli, assembly 1, front view.
CMT2-Fab heavy chain in PDB entry 7zli, assembly 1, side view.
CMT2-Fab heavy chain in PDB entry 7zli, assembly 1, top view.
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Anti-Fab nanobody
Chain: K
Length: 123 amino acids
Theoretical weight: 13.39 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
InterPro:
Anti-Fab nanobody in PDB entry 7zli, assembly 1, front view.
Anti-Fab nanobody in PDB entry 7zli, assembly 1, side view.
Anti-Fab nanobody in PDB entry 7zli, assembly 1, top view.
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Ig-like domain-containing protein
Chain: L
Length: 215 amino acids
Theoretical weight: 23.24 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7Z3Y4 (Residues: 23-236; Coverage: 100%)
Pfam:
InterPro:
Ig-like domain-containing protein in PDB entry 7zli, assembly 1, front view.
Ig-like domain-containing protein in PDB entry 7zli, assembly 1, side view.
Ig-like domain-containing protein in PDB entry 7zli, assembly 1, top view.
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C-mannosyltransferase dpy-19
Chain: A
Length: 707 amino acids
Theoretical weight: 80.89 KDa
Source organism: Caenorhabditis elegans
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P34413 (Residues: 1-683; Coverage: 100%)
Gene names: F22B7.10, dpy-19
Pfam: Q-cell neuroblast polarisation
InterPro:
C-mannosyltransferase dpy-19 in PDB entry 7zli, assembly 1, front view.
C-mannosyltransferase dpy-19 in PDB entry 7zli, assembly 1, side view.
C-mannosyltransferase dpy-19 in PDB entry 7zli, assembly 1, top view.
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