7ZLH | pdb_00007zlh

Cryo-EM structure of C-mannosyltransferase CeDPY19, in apo state, bound to CMT2-Fab and anti-Fab nanobody

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
C [auth L]	C1-set_4	e7zlhL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
C [auth L]	V-set	e7zlhL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B [auth K]	V-set_12	e7zlhK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
A [auth H]	C1-set_1	e7zlhH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
A [auth H]	V-set_12	e7zlhH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L]	Light Chain	IGKV1	Kappa	c-mannosyltransferase dpy-19	SAbDab (2025-12-12)
B [auth K]	Heavy Chain	IGHV1	-	-	SAbDab (2025-12-12)
A [auth H]	Heavy Chain	IGHV3	-	c-mannosyltransferase dpy-19	SAbDab (2025-12-12)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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 primary metabolic process metabolic process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development	cellular anatomical structure intracellular anatomical structure perinuclear region of cytoplasm cytoplasm membrane-bounded organelle organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cellular anatomical structure intracellular anatomical structure perinuclear region of cytoplasm cytoplasm membrane-bounded organelle organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane
C [auth L]	CMT2-Fab light chain	-	-	-
B [auth K]	Anti-Fab nanobody	-	-	-
A [auth H]	CMT2-Fab heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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
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 R01GM157729.