7ZLJ

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

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth H]	PF07654	e7zljH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A [auth H]	PF07686	e7zljH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth K]	PF07686	e7zljK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth L]	PF07654	e7zljL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth L]	PF07686	e7zljL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H]	Heavy Chain	IGHV3	-	c-mannosyltransferase dpy-19	SAbDab (2024-05-10)
B [auth K]	Heavy Chain	IGHV1	-	-	SAbDab (2024-05-10)
C [auth L]	Light Chain	IGKV1	Kappa	c-mannosyltransferase dpy-19	SAbDab (2024-05-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth L]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
C [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
D [auth A]	PF10034	Q-cell neuroblast polarisation (Dpy19)	Q-cell neuroblast polarisation	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H]	CMT2-Fab heavy chain	-	-	-
B [auth K]	Anti-Fab nanobody	-	-	-
C [auth L]	CMT2-Fab light chain	-	-	extracellular region cellular anatomical entity
D [auth A]	C-mannosyltransferase dpy-19	glycosyltransferase activity mannosyltransferase activity transferase activity hexosyltransferase activity catalytic activity	developmental process cellular developmental process cell differentiation cellular process carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development protein mannosylation developmental process cellular developmental process cell differentiation cellular process carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development protein mannosylation cellular biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process peptidyl-amino acid modification organic substance biosynthetic process protein C-linked glycosylation via tryptophan protein metabolic process protein modification process protein C-linked glycosylation peptidyl-tryptophan modification carbohydrate derivative biosynthetic process organonitrogen compound metabolic process cellular metabolic process glycoprotein biosynthetic process glycoprotein metabolic process protein glycosylation macromolecule biosynthetic process biosynthetic process glycosylation mannosylation protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan macromolecule modification macromolecule glycosylation macromolecule metabolic process	intracellular anatomical structure perinuclear region of cytoplasm cytoplasm cellular anatomical entity membrane-bounded organelle organelle inner membrane nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle intracellular anatomical structure perinuclear region of cytoplasm cytoplasm cellular anatomical entity membrane-bounded organelle organelle inner membrane nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear inner membrane nuclear envelope organelle membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
E [auth P]	synthetic octapeptide WEHI 1886493	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth L]	IPR003597	Immunoglobulin C1-set	Domain
C [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth L]	IPR003599	Immunoglobulin subtype	Domain
C [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth L]	IPR007110	Immunoglobulin-like domain	Domain
C [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D [auth A]	IPR011330	Glycoside hydrolase/deacetylase, beta/alpha-barrel	Homologous Superfamily
D [auth A]	IPR047462	C-mannosyltransferase Dpy19	Family
D [auth A]	IPR018732	Dpy-19/Dpy-19-like	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
C [auth L], D [auth A]	OPM	Transmembrane	Alpha-helical polytopic	Glycosyl transferase GT-C superfamily	C-mannosyltransferase Dpy19-like

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
C [auth L], D [auth A]	PDBTM	Annotated as membrane protein by PDBTM

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.