6TYL | pdb_00006tyl

Crystal structure of mammalian Ric-8A:Galpha(i):nanobody complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth G]	SCOP2B Superfamily	Ras-like P-loop GTPases	8019719	3002022	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Ras-like P-loop GTPases	8019719	3002022	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I [auth G]	Ras	e6tylG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
H [auth B]	Ras	e6tylB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
G [auth I]	V-set_12	e6tylI1	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)
F [auth D]	V-set_12	e6tylD1	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)
E [auth J]	V-set_1	e6tylJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
D [auth E]	V-set_1	e6tylE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_1	ECOD (1.6)
C [auth H]	V-set_8	e6tylH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth C]	V-set_8	e6tylC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth F]	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (utative)
A	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
F [auth D], G [auth I]	Heavy Chain	IGHV1	-	resistance to inhibitors of cholinesterase 8 homolog a (c.elegans)	SAbDab (2025-11-28)
D [auth E], E [auth J]	Heavy Chain	IGHV1	-	resistance to inhibitors of cholinesterase 8 homolog a (c.elegans)	SAbDab (2025-11-28)
B [auth C], C [auth H]	Heavy Chain	IGHV1	-	resistance to inhibitors of cholinesterase 8 homolog a (c.elegans)	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, J [auth F]	PF10165	Guanine nucleotide exchange factor synembryn (Ric8)	Guanine nucleotide exchange factor synembryn	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth B], I [auth G]	Guanine nucleotide-binding protein G(i) subunit alpha-1	D2 dopamine receptor binding protein binding binding signaling receptor binding G protein-coupled receptor binding dopamine receptor binding enzyme regulator activity cyclase regulator activity molecular function regulator activity adenylate cyclase regulator activity GTPase activating protein binding guanyl nucleotide binding GTP binding nucleotide binding D2 dopamine receptor binding protein binding binding signaling receptor binding G protein-coupled receptor binding dopamine receptor binding enzyme regulator activity cyclase regulator activity molecular function regulator activity adenylate cyclase regulator activity GTPase activating protein binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding magnesium ion binding metal ion binding GDP binding G protein-coupled serotonin receptor binding protein-containing complex binding G-protein beta/gamma-subunit complex binding pyrophosphatase activity GTPase activity G protein 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	protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle cellular process protein localization to postsynapse intracellular protein localization regulation of biological quality protein localization to cell junction receptor localization to synapse cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling adenylate cyclase-inhibiting serotonin receptor signaling pathway G protein-coupled serotonin receptor signaling pathway cell communication adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction cell division leukocyte migration immune system process mononuclear cell migration lymphocyte migration cell migration T cell migration cell motility regulation of steroid biosynthetic process regulation of cholesterol biosynthetic process regulation of cholesterol metabolic process steroid metabolic process regulation of lipid metabolic process sterol metabolic process positive regulation of biological process cholesterol metabolic process lipid biosynthetic process alcohol metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process positive regulation of lipid metabolic process small molecule metabolic process steroid biosynthetic process positive regulation of cellular process regulation of biosynthetic process secondary alcohol biosynthetic process regulation of alcohol biosynthetic process small molecule biosynthetic process regulation of steroid metabolic process cholesterol biosynthetic process positive regulation of cholesterol biosynthetic process primary metabolic process secondary alcohol metabolic process positive regulation of steroid biosynthetic process biosynthetic process sterol biosynthetic process positive regulation of lipid biosynthetic process regulation of sterol biosynthetic process alcohol biosynthetic process positive regulation of cholesterol metabolic process positive regulation of steroid metabolic process metabolic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process regulation of metabolic process positive regulation of alcohol biosynthetic process positive regulation of sterol biosynthetic process lipid metabolic process regulation of cytoskeleton organization regulation of cellular component organization microtubule cytoskeleton organization regulation of mitotic spindle organization mitotic cell cycle cellular component organization cell cycle cellular component organization or biogenesis regulation of cell cycle microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process regulation of cell cycle process regulation of microtubule-based process regulation of spindle organization regulation of organelle organization mitotic spindle organization organelle organization mitotic cell cycle process microtubule-based process cytoskeleton organization regulation of microtubule cytoskeleton organization positive regulation of protein localization to cell periphery regulation of localization regulation of protein localization positive regulation of protein localization to cell cortex regulation of protein localization to cell periphery regulation of protein localization to cell cortex positive regulation of protein localization protein localization to cell cortex response to ketone response to prostaglandin response to lipid response to hormone response to chemical response to endogenous stimulus response to alcohol response to prostaglandin E response to oxygen-containing compound trans-synaptic signaling regulation of signaling negative regulation of signaling modulation of chemical synaptic transmission negative regulation of biological process cell-cell signaling negative regulation of synaptic transmission negative regulation of cell communication chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling negative regulation of cellular process regulation of cell communication cellular response to forskolin cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to forskolin cellular response to lipid cellular response to ketone	midbody cellular anatomical structure cell periphery cell cortex intracellular anatomical structure cytoplasm protein-containing complex extrinsic component of plasma membrane catalytic complex plasma membrane protein complex cytoplasmic side of membrane membrane plasma membrane membrane protein complex midbody cellular anatomical structure cell periphery cell cortex intracellular anatomical structure cytoplasm protein-containing complex extrinsic component of plasma membrane catalytic complex plasma membrane protein complex cytoplasmic side of membrane membrane plasma membrane membrane protein complex heterotrimeric G-protein complex side of membrane cytoplasmic side of plasma membrane GTPase complex extrinsic component of membrane extrinsic component of cytoplasmic side of plasma membrane intracellular organelle centrosome microtubule organizing center cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytosol synapse cell junction glutamatergic synapse postsynapse membrane-bounded organelle nucleus intracellular membrane-bounded organelle
F [auth D], G [auth I]	Nanobody C	-	-	-
D [auth E], E [auth J]	Nanobody B	-	-	-
B [auth C], C [auth H]	Nanobody A	-	-	-
A, J [auth F]	Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)	protein binding binding G-protein alpha-subunit binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity enzyme activator activity GTPase activator activity molecular function activator activity protein folding chaperone	developmental process multicellular organismal process embryonic morphogenesis embryo development gastrulation multicellular organism development anatomical structure morphogenesis ameboidal-type cell migration anatomical structure development cell migration cellular process cell motility cell migration involved in gastrulation cellular response to stimulus developmental process multicellular organismal process embryonic morphogenesis embryo development gastrulation multicellular organism development anatomical structure morphogenesis ameboidal-type cell migration anatomical structure development cell migration cellular process cell motility cell migration involved in gastrulation cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction cell-cell adhesion involved in gastrulation cell adhesion cell-cell adhesion response to light stimulus response to radiation response to abiotic stimulus vasculature development system development circulatory system development system process learning learning or memory nervous system process visual learning visual behavior cognition associative learning behavior embryo development ending in birth or egg hatching chordate embryonic development in utero embryonic development cellular component organization extracellular matrix organization cellular component organization or biogenesis basement membrane organization extracellular structure organization external encapsulating structure organization	cellular anatomical structure membrane cell periphery cell cortex intracellular anatomical structure cytoplasm plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H [auth B], I [auth G]	IPR001019	Guanine nucleotide binding protein (G-protein), alpha subunit	Family
H [auth B], I [auth G]	IPR011025	G protein alpha subunit, helical insertion	Homologous Superfamily
H [auth B], I [auth G]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
H [auth B], I [auth G]	IPR001408	G-protein alpha subunit, group I	Family
A, J [auth F]	IPR016024	Armadillo-type fold	Homologous Superfamily
A, J [auth F]	IPR008376	Chaperone Ric-8 A/B	Domain
A, J [auth F]	IPR019318	Guanine nucleotide exchange factor, Ric8	Family
A, J [auth F]	IPR011989	Armadillo-like helical	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, J [auth F]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
A, J [auth F]	TPO	Parent Component: THR RESID: AA0037 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047

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.