5LDD

Crystal structure of the heterodimeric GEF Mon1-Ccz1 in complex with Ypt7

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d5lddc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Thermochaetoides thermophila DSM 1495 ) [TaxId: 759272 ],	SCOPe (2.08)
F	d5lddf_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Thermochaetoides thermophila DSM 1495 ) [TaxId: 759272 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF19036	e5lddA1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: PF19036	ECOD (1.6)
D	PF19036	e5lddD1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: PF19036	ECOD (1.6)
C	PF00071	e5lddC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00071	ECOD (1.6)
F	PF00071	e5lddF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00071	ECOD (1.6)
B	PF19031	e5lddB1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: PF19031	ECOD (1.6)
E	PF19031	e5lddE1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: PF19031	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF19036	First Longin domain of FUZ, MON1 and HPS1 (Fuz_longin_1)	First Longin domain of FUZ, MON1 and HPS1	This entry is specific to the first Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) family, including protein sequences of FUZ, MON1 and HPS1 families [1,3,5]. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for ...	This entry is specific to the first Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) family, including protein sequences of FUZ, MON1 and HPS1 families [1,3,5]. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking [2]. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules [3]. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia [4,6].	Domain
C, F	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain
B, E	PF19031	First Longin domain of INTU, CCZ1 and HPS4 (Intu_longin_1)	First Longin domain of INTU, CCZ1 and HPS4	This entry is specific to the first Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1/CCZ1) family, including protein sequences of INTU, CCZ1 and HPS4 families [1,3,5]. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) fo ...	This entry is specific to the first Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1/CCZ1) family, including protein sequences of INTU, CCZ1 and HPS4 families [1,3,5]. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking [2]. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules [3]. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia [4,6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Mon1	-	localization transport cellular process establishment of localization vesicle-mediated transport protein localization establishment of protein localization cellular localization nitrogen compound transport protein targeting organic substance transport establishment of protein localization to vacuole protein localization to vacuole intracellular transport localization transport cellular process establishment of localization vesicle-mediated transport protein localization establishment of protein localization cellular localization nitrogen compound transport protein targeting organic substance transport establishment of protein localization to vacuole protein localization to vacuole intracellular transport establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle establishment of localization in cell vacuolar transport protein targeting to vacuole intracellular protein transport cellular catabolic process catabolic process cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane endosome membrane endosome vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane endosome membrane endosome multivesicular body membrane intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle multivesicular body
C, F	Rab small monomeric GTPase-like protein	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	-	-
B, E	Ccz1	-	localization transport cellular process establishment of localization vesicle-mediated transport	membrane-bounded organelle protein-containing complex intracellular anatomical structure endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome Mon1-Ccz1 complex cytoplasm membrane-bounded organelle protein-containing complex intracellular anatomical structure endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome Mon1-Ccz1 complex cytoplasm vesicle guanyl-nucleotide exchange factor complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR004353	Vacuolar fusion protein Mon1	Family
A, D	IPR043970	FUZ/MON1/HPS1, third Longin domain	Domain
A, D	IPR043972	FUZ/MON1/HPS1, first Longin domain	Domain
A, D	IPR043971	FUZ/MON1/HPS1, second Longin domain	Domain
C, F	IPR001806	Small GTPase	Family
C, F	IPR005225	Small GTP-binding protein domain	Domain
C, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, E	IPR043987	CCZ1/INTU/HSP4, first Longin domain	Domain
B, E	IPR013176	Vacuolar fusion protein Ccz1	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.