9ZPD

Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004674	molecular_function	protein serine/threonine kinase activity
A	0005737	cellular_component	cytoplasm
A	0005770	cellular_component	late endosome
A	0005776	cellular_component	autophagosome
A	0005856	cellular_component	cytoskeleton
A	0005929	cellular_component	cilium
A	0016020	cellular_component	membrane
A	0035032	cellular_component	phosphatidylinositol 3-kinase complex, class III
B	0000045	biological_process	autophagosome assembly
B	0000407	cellular_component	phagophore assembly site
B	0000425	biological_process	pexophagy
B	0004672	molecular_function	protein kinase activity
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005768	cellular_component	endosome
B	0005770	cellular_component	late endosome
B	0005776	cellular_component	autophagosome
B	0005777	cellular_component	peroxisome
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0005930	cellular_component	axoneme
B	0006622	biological_process	protein targeting to lysosome
B	0006897	biological_process	endocytosis
B	0006914	biological_process	autophagy
B	0007032	biological_process	endosome organization
B	0010506	biological_process	regulation of autophagy
B	0016020	cellular_component	membrane
B	0016236	biological_process	macroautophagy
B	0016241	biological_process	regulation of macroautophagy
B	0016301	molecular_function	kinase activity
B	0016303	molecular_function	1-phosphatidylinositol-3-kinase activity
B	0016485	biological_process	protein processing
B	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
B	0030496	cellular_component	midbody
B	0030670	cellular_component	phagocytic vesicle membrane
B	0032465	biological_process	regulation of cytokinesis
B	0034271	cellular_component	phosphatidylinositol 3-kinase complex, class III, type I
B	0034272	cellular_component	phosphatidylinositol 3-kinase complex, class III, type II
B	0035032	cellular_component	phosphatidylinositol 3-kinase complex, class III
B	0036092	biological_process	phosphatidylinositol-3-phosphate biosynthetic process
B	0042149	biological_process	cellular response to glucose starvation
B	0043201	biological_process	response to L-leucine
B	0043491	biological_process	phosphatidylinositol 3-kinase/protein kinase B signal transduction
B	0044754	cellular_component	autolysosome
B	0044829	biological_process	host-mediated activation of viral genome replication
B	0045022	biological_process	early endosome to late endosome transport
B	0045335	cellular_component	phagocytic vesicle
B	0045954	biological_process	positive regulation of natural killer cell mediated cytotoxicity
B	0046854	biological_process	phosphatidylinositol phosphate biosynthetic process
B	0048015	biological_process	phosphatidylinositol-mediated signaling
B	0048488	biological_process	synaptic vesicle endocytosis
B	0052742	molecular_function	phosphatidylinositol kinase activity
B	0097352	biological_process	autophagosome maturation
B	0098794	cellular_component	postsynapse
B	0098830	cellular_component	presynaptic endosome
B	0098845	cellular_component	postsynaptic endosome
B	0098978	cellular_component	glutamatergic synapse
B	0098982	cellular_component	GABA-ergic synapse
B	1903061	biological_process	positive regulation of protein lipidation
C	0000149	molecular_function	SNARE binding
C	0000323	cellular_component	lytic vacuole
C	0000421	cellular_component	autophagosome membrane
C	0000775	cellular_component	chromosome, centromeric region
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005764	cellular_component	lysosome
C	0005768	cellular_component	endosome
C	0005769	cellular_component	early endosome
C	0005770	cellular_component	late endosome
C	0005776	cellular_component	autophagosome
C	0005783	cellular_component	endoplasmic reticulum
C	0005813	cellular_component	centrosome
C	0006281	biological_process	DNA repair
C	0006890	biological_process	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
C	0006914	biological_process	autophagy
C	0007051	biological_process	spindle organization
C	0007059	biological_process	chromosome segregation
C	0007098	biological_process	centrosome cycle
C	0010506	biological_process	regulation of autophagy
C	0016192	biological_process	vesicle-mediated transport
C	0017124	molecular_function	SH3 domain binding
C	0030496	cellular_component	midbody
C	0031410	cellular_component	cytoplasmic vesicle
C	0032465	biological_process	regulation of cytokinesis
C	0032801	biological_process	receptor catabolic process
C	0032991	cellular_component	protein-containing complex
C	0033116	cellular_component	endoplasmic reticulum-Golgi intermediate compartment membrane
C	0035493	biological_process	SNARE complex assembly
C	0036092	biological_process	phosphatidylinositol-3-phosphate biosynthetic process
C	0043933	biological_process	protein-containing complex organization
C	0045335	cellular_component	phagocytic vesicle
C	0051684	biological_process	maintenance of Golgi location
C	0070418	cellular_component	DNA-dependent protein kinase complex
C	0071900	biological_process	regulation of protein serine/threonine kinase activity
C	0071985	biological_process	multivesicular body sorting pathway
C	0097352	biological_process	autophagosome maturation
C	0097680	biological_process	double-strand break repair via classical nonhomologous end joining
C	1901098	biological_process	positive regulation of autophagosome maturation
D	0000045	biological_process	autophagosome assembly
D	0000407	cellular_component	phagophore assembly site
D	0000423	biological_process	mitophagy
D	0001666	biological_process	response to hypoxia
D	0002753	biological_process	cytoplasmic pattern recognition receptor signaling pathway
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005768	cellular_component	endosome
D	0005776	cellular_component	autophagosome
D	0005783	cellular_component	endoplasmic reticulum
D	0005789	cellular_component	endoplasmic reticulum membrane
D	0005794	cellular_component	Golgi apparatus
D	0005802	cellular_component	trans-Golgi network
D	0005829	cellular_component	cytosol
D	0006622	biological_process	protein targeting to lysosome
D	0006914	biological_process	autophagy
D	0006968	biological_process	cellular defense response
D	0006995	biological_process	cellular response to nitrogen starvation
D	0007080	biological_process	mitotic metaphase chromosome alignment
D	0007254	biological_process	JNK cascade
D	0007623	biological_process	circadian rhythm
D	0009410	biological_process	response to xenobiotic stimulus
D	0010008	cellular_component	endosome membrane
D	0010040	biological_process	response to iron(II) ion
D	0010288	biological_process	response to lead ion
D	0010506	biological_process	regulation of autophagy
D	0010508	biological_process	positive regulation of autophagy
D	0016236	biological_process	macroautophagy
D	0016241	biological_process	regulation of macroautophagy
D	0016604	cellular_component	nuclear body
D	0019901	molecular_function	protein kinase binding
D	0030425	cellular_component	dendrite
D	0030674	molecular_function	protein-macromolecule adaptor activity
D	0031410	cellular_component	cytoplasmic vesicle
D	0031625	molecular_function	ubiquitin protein ligase binding
D	0031667	biological_process	response to nutrient levels
D	0031966	cellular_component	mitochondrial membrane
D	0032465	biological_process	regulation of cytokinesis
D	0032473	cellular_component	cytoplasmic side of mitochondrial outer membrane
D	0032801	biological_process	receptor catabolic process
D	0032991	cellular_component	protein-containing complex
D	0033197	biological_process	response to vitamin E
D	0034198	biological_process	cellular response to amino acid starvation
D	0034271	cellular_component	phosphatidylinositol 3-kinase complex, class III, type I
D	0034272	cellular_component	phosphatidylinositol 3-kinase complex, class III, type II
D	0035032	cellular_component	phosphatidylinositol 3-kinase complex, class III
D	0036092	biological_process	phosphatidylinositol-3-phosphate biosynthetic process
D	0038066	biological_process	p38MAPK cascade
D	0042149	biological_process	cellular response to glucose starvation
D	0042802	molecular_function	identical protein binding
D	0043066	biological_process	negative regulation of apoptotic process
D	0043069	biological_process	negative regulation of programmed cell death
D	0043548	molecular_function	phosphatidylinositol 3-kinase binding
D	0043652	biological_process	engulfment of apoptotic cell
D	0045022	biological_process	early endosome to late endosome transport
D	0045324	biological_process	late endosome to vacuole transport
D	0045335	cellular_component	phagocytic vesicle
D	0051020	molecular_function	GTPase binding
D	0051897	biological_process	positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
D	0060090	molecular_function	molecular adaptor activity
D	0060395	biological_process	SMAD protein signal transduction
D	0062029	biological_process	positive regulation of stress granule assembly
D	0065003	biological_process	protein-containing complex assembly
D	0070301	biological_process	cellular response to hydrogen peroxide
D	0071275	biological_process	cellular response to aluminum ion
D	0071280	biological_process	cellular response to copper ion
D	0071364	biological_process	cellular response to epidermal growth factor stimulus
D	0090650	biological_process	cellular response to oxygen-glucose deprivation
D	0097352	biological_process	autophagosome maturation
D	0098780	biological_process	response to mitochondrial depolarisation
D	1902425	biological_process	positive regulation of attachment of mitotic spindle microtubules to kinetochore
D	1905672	biological_process	negative regulation of lysosome organization
D	2000786	biological_process	positive regulation of autophagosome assembly
D	2001244	biological_process	positive regulation of intrinsic apoptotic signaling pathway
E	0000045	biological_process	autophagosome assembly
E	0000407	cellular_component	phagophore assembly site
E	0000423	biological_process	mitophagy
E	0001666	biological_process	response to hypoxia
E	0002753	biological_process	cytoplasmic pattern recognition receptor signaling pathway
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005739	cellular_component	mitochondrion
E	0005768	cellular_component	endosome
E	0005776	cellular_component	autophagosome
E	0005783	cellular_component	endoplasmic reticulum
E	0005789	cellular_component	endoplasmic reticulum membrane
E	0005794	cellular_component	Golgi apparatus
E	0005802	cellular_component	trans-Golgi network
E	0005829	cellular_component	cytosol
E	0006622	biological_process	protein targeting to lysosome
E	0006914	biological_process	autophagy
E	0006968	biological_process	cellular defense response
E	0006995	biological_process	cellular response to nitrogen starvation
E	0007080	biological_process	mitotic metaphase chromosome alignment
E	0007254	biological_process	JNK cascade
E	0007623	biological_process	circadian rhythm
E	0009410	biological_process	response to xenobiotic stimulus
E	0010008	cellular_component	endosome membrane
E	0010040	biological_process	response to iron(II) ion
E	0010288	biological_process	response to lead ion
E	0010506	biological_process	regulation of autophagy
E	0010508	biological_process	positive regulation of autophagy
E	0016236	biological_process	macroautophagy
E	0016241	biological_process	regulation of macroautophagy
E	0016604	cellular_component	nuclear body
E	0019901	molecular_function	protein kinase binding
E	0030425	cellular_component	dendrite
E	0030674	molecular_function	protein-macromolecule adaptor activity
E	0031410	cellular_component	cytoplasmic vesicle
E	0031625	molecular_function	ubiquitin protein ligase binding
E	0031667	biological_process	response to nutrient levels
E	0031966	cellular_component	mitochondrial membrane
E	0032465	biological_process	regulation of cytokinesis
E	0032473	cellular_component	cytoplasmic side of mitochondrial outer membrane
E	0032801	biological_process	receptor catabolic process
E	0032991	cellular_component	protein-containing complex
E	0033197	biological_process	response to vitamin E
E	0034198	biological_process	cellular response to amino acid starvation
E	0034271	cellular_component	phosphatidylinositol 3-kinase complex, class III, type I
E	0034272	cellular_component	phosphatidylinositol 3-kinase complex, class III, type II
E	0035032	cellular_component	phosphatidylinositol 3-kinase complex, class III
E	0036092	biological_process	phosphatidylinositol-3-phosphate biosynthetic process
E	0038066	biological_process	p38MAPK cascade
E	0042149	biological_process	cellular response to glucose starvation
E	0042802	molecular_function	identical protein binding
E	0043066	biological_process	negative regulation of apoptotic process
E	0043069	biological_process	negative regulation of programmed cell death
E	0043548	molecular_function	phosphatidylinositol 3-kinase binding
E	0043652	biological_process	engulfment of apoptotic cell
E	0045022	biological_process	early endosome to late endosome transport
E	0045324	biological_process	late endosome to vacuole transport
E	0045335	cellular_component	phagocytic vesicle
E	0051020	molecular_function	GTPase binding
E	0051897	biological_process	positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
E	0060090	molecular_function	molecular adaptor activity
E	0060395	biological_process	SMAD protein signal transduction
E	0062029	biological_process	positive regulation of stress granule assembly
E	0065003	biological_process	protein-containing complex assembly
E	0070301	biological_process	cellular response to hydrogen peroxide
E	0071275	biological_process	cellular response to aluminum ion
E	0071280	biological_process	cellular response to copper ion
E	0071364	biological_process	cellular response to epidermal growth factor stimulus
E	0090650	biological_process	cellular response to oxygen-glucose deprivation
E	0097352	biological_process	autophagosome maturation
E	0098780	biological_process	response to mitochondrial depolarisation
E	1902425	biological_process	positive regulation of attachment of mitotic spindle microtubules to kinetochore
E	1905672	biological_process	negative regulation of lysosome organization
E	2000786	biological_process	positive regulation of autophagosome assembly
E	2001244	biological_process	positive regulation of intrinsic apoptotic signaling pathway

Functional Information from PROSITE/UniProt

site_id	PS00108
Number of Residues	13
Details	PROTEIN_KINASE_ST Serine/Threonine protein kinases active-site signature. VrHgDIKteNVMV

Chain	Residue	Details
A	VAL144-VAL156

---

site_id	PS00678
Number of Residues	15
Details	WD_REPEATS_1 Trp-Asp (WD) repeats signature. IAAVqgNnEVSMWDM

Chain	Residue	Details
A	ILE1201-MET1215
A	LEU1256-LEU1270

---

site_id	PS00915
Number of Residues	15
Details	PI3_4_KINASE_1 Phosphatidylinositol 3- and 4-kinases signature 1. FKhg.DDLRQDqlilQ

Chain	Residue	Details
B	PHE635-GLN649

---

site_id	PS00916
Number of Residues	21
Details	PI3_4_KINASE_2 Phosphatidylinositol 3- and 4-kinases signature 2. ScAgycVitYILgVgDRHldN

Chain	Residue	Details
B	SER728-ASN748

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by AMPK","evidences":[{"source":"UniProtKB","id":"Q6PF93","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	69
Details	Region: {"description":"Sufficient for interaction with STX7; VTI1B AND STX8","evidences":[{"source":"PubMed","id":"24550300","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	172
Details	Region: {"description":"Sufficient for interaction with VPS16, required for interaction with CEP63","evidences":[{"source":"PubMed","id":"18552835","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22542840","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	209
Details	Coiled coil: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	47
Details	Region: {"description":"Interaction with BCL2 and BCL2L1 isoform Bcl-X(L)","evidences":[{"source":"PubMed","id":"17446862","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"31123703","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by DAPK1","evidences":[{"source":"PubMed","id":"19180116","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"28445460","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"23974797","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---