8FO2

Cryo-EM structure of Rab29-LRRK2 complex in the LRRK2 monomer state

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0003924	molecular_function	GTPase activity
B	0005525	molecular_function	GTP binding
B	0005794	cellular_component	Golgi apparatus
B	0005802	cellular_component	trans-Golgi network
B	0016192	biological_process	vesicle-mediated transport
B	0031982	cellular_component	vesicle
E	0000139	cellular_component	Golgi membrane
E	0000149	molecular_function	SNARE binding
E	0000165	biological_process	MAPK cascade
E	0000166	molecular_function	nucleotide binding
E	0000287	molecular_function	magnesium ion binding
E	0003779	molecular_function	actin binding
E	0003924	molecular_function	GTPase activity
E	0004672	molecular_function	protein kinase activity
E	0004674	molecular_function	protein serine/threonine kinase activity
E	0004706	molecular_function	JUN kinase kinase kinase activity
E	0004709	molecular_function	MAP kinase kinase kinase activity
E	0005096	molecular_function	GTPase activator activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005525	molecular_function	GTP binding
E	0005615	cellular_component	extracellular space
E	0005737	cellular_component	cytoplasm
E	0005739	cellular_component	mitochondrion
E	0005741	cellular_component	mitochondrial outer membrane
E	0005743	cellular_component	mitochondrial inner membrane
E	0005759	cellular_component	mitochondrial matrix
E	0005764	cellular_component	lysosome
E	0005768	cellular_component	endosome
E	0005783	cellular_component	endoplasmic reticulum
E	0005789	cellular_component	endoplasmic reticulum membrane
E	0005794	cellular_component	Golgi apparatus
E	0005798	cellular_component	Golgi-associated vesicle
E	0005802	cellular_component	trans-Golgi network
E	0005829	cellular_component	cytosol
E	0005856	cellular_component	cytoskeleton
E	0005886	cellular_component	plasma membrane
E	0005902	cellular_component	microvillus
E	0006468	biological_process	protein phosphorylation
E	0006897	biological_process	endocytosis
E	0006914	biological_process	autophagy
E	0006979	biological_process	response to oxidative stress
E	0007005	biological_process	mitochondrion organization
E	0007029	biological_process	endoplasmic reticulum organization
E	0007030	biological_process	Golgi organization
E	0007040	biological_process	lysosome organization
E	0007166	biological_process	cell surface receptor signaling pathway
E	0007254	biological_process	JNK cascade
E	0007266	biological_process	Rho protein signal transduction
E	0007283	biological_process	spermatogenesis
E	0007528	biological_process	neuromuscular junction development
E	0008017	molecular_function	microtubule binding
E	0008021	cellular_component	synaptic vesicle
E	0008104	biological_process	intracellular protein localization
E	0008340	biological_process	determination of adult lifespan
E	0009267	biological_process	cellular response to starvation
E	0009653	biological_process	anatomical structure morphogenesis
E	0009968	biological_process	negative regulation of signal transduction
E	0010468	biological_process	regulation of gene expression
E	0010506	biological_process	regulation of autophagy
E	0010508	biological_process	positive regulation of autophagy
E	0010955	biological_process	negative regulation of protein processing
E	0010977	biological_process	negative regulation of neuron projection development
E	0014041	biological_process	regulation of neuron maturation
E	0015631	molecular_function	tubulin binding
E	0016192	biological_process	vesicle-mediated transport
E	0016242	biological_process	negative regulation of macroautophagy
E	0016301	molecular_function	kinase activity
E	0016740	molecular_function	transferase activity
E	0016787	molecular_function	hydrolase activity
E	0017075	molecular_function	syntaxin-1 binding
E	0019722	biological_process	calcium-mediated signaling
E	0021756	biological_process	striatum development
E	0021772	biological_process	olfactory bulb development
E	0022028	biological_process	tangential migration from the subventricular zone to the olfactory bulb
E	0030154	biological_process	cell differentiation
E	0030159	molecular_function	signaling receptor complex adaptor activity
E	0030162	biological_process	regulation of proteolysis
E	0030182	biological_process	neuron differentiation
E	0030276	molecular_function	clathrin binding
E	0030424	cellular_component	axon
E	0030425	cellular_component	dendrite
E	0030426	cellular_component	growth cone
E	0030672	cellular_component	synaptic vesicle membrane
E	0031267	molecular_function	small GTPase binding
E	0031344	biological_process	regulation of cell projection organization
E	0031398	biological_process	positive regulation of protein ubiquitination
E	0031410	cellular_component	cytoplasmic vesicle
E	0031647	biological_process	regulation of protein stability
E	0031966	cellular_component	mitochondrial membrane
E	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
E	0032473	cellular_component	cytoplasmic side of mitochondrial outer membrane
E	0032760	biological_process	positive regulation of tumor necrosis factor production
E	0032839	cellular_component	dendrite cytoplasm
E	0034211	molecular_function	GTP-dependent protein kinase activity
E	0034260	biological_process	negative regulation of GTPase activity
E	0034599	biological_process	cellular response to oxidative stress
E	0034614	biological_process	cellular response to reactive oxygen species
E	0035542	biological_process	regulation of SNARE complex assembly
E	0035556	biological_process	intracellular signal transduction
E	0035564	biological_process	regulation of kidney size
E	0035640	biological_process	exploration behavior
E	0035641	biological_process	locomotory exploration behavior
E	0035751	biological_process	regulation of lysosomal lumen pH
E	0036479	molecular_function	peroxidase inhibitor activity
E	0039706	molecular_function	co-receptor binding
E	0040012	biological_process	regulation of locomotion
E	0042391	biological_process	regulation of membrane potential
E	0042802	molecular_function	identical protein binding
E	0042803	molecular_function	protein homodimerization activity
E	0043005	cellular_component	neuron projection
E	0043025	cellular_component	neuronal cell body
E	0043068	biological_process	positive regulation of programmed cell death
E	0043195	cellular_component	terminal bouton
E	0043204	cellular_component	perikaryon
E	0043410	biological_process	positive regulation of MAPK cascade
E	0044325	molecular_function	transmembrane transporter binding
E	0044753	cellular_component	amphisome
E	0044754	cellular_component	autolysosome
E	0045121	cellular_component	membrane raft
E	0045202	cellular_component	synapse
E	0045335	cellular_component	phagocytic vesicle
E	0046039	biological_process	GTP metabolic process
E	0046777	biological_process	protein autophosphorylation
E	0048312	biological_process	intracellular distribution of mitochondria
E	0048513	biological_process	animal organ development
E	0048812	biological_process	neuron projection morphogenesis
E	0050804	biological_process	modulation of chemical synaptic transmission
E	0051018	molecular_function	protein kinase A binding
E	0051239	biological_process	regulation of multicellular organismal process
E	0051247	biological_process	positive regulation of protein metabolic process
E	0051646	biological_process	mitochondrion localization
E	0051900	biological_process	regulation of mitochondrial depolarization
E	0051966	biological_process	regulation of synaptic transmission, glutamatergic
E	0060070	biological_process	canonical Wnt signaling pathway
E	0060079	biological_process	excitatory postsynaptic potential
E	0060159	biological_process	regulation of dopamine receptor signaling pathway
E	0060161	biological_process	positive regulation of dopamine receptor signaling pathway
E	0060627	biological_process	regulation of vesicle-mediated transport
E	0060628	biological_process	regulation of ER to Golgi vesicle-mediated transport
E	0060828	biological_process	regulation of canonical Wnt signaling pathway
E	0061001	biological_process	regulation of dendritic spine morphogenesis
E	0070013	cellular_component	intracellular organelle lumen
E	0070062	cellular_component	extracellular exosome
E	0070585	biological_process	protein localization to mitochondrion
E	0070971	cellular_component	endoplasmic reticulum exit site
E	0070973	biological_process	protein localization to endoplasmic reticulum exit site
E	0071287	biological_process	cellular response to manganese ion
E	0090140	biological_process	regulation of mitochondrial fission
E	0090263	biological_process	positive regulation of canonical Wnt signaling pathway
E	0090394	biological_process	negative regulation of excitatory postsynaptic potential
E	0097413	cellular_component	Lewy body
E	0097487	cellular_component	multivesicular body, internal vesicle
E	0098794	cellular_component	postsynapse
E	0098978	cellular_component	glutamatergic synapse
E	0099400	cellular_component	caveola neck
E	0099523	cellular_component	presynaptic cytosol
E	0106310	molecular_function	protein serine kinase activity
E	0140058	biological_process	neuron projection arborization
E	0141161	biological_process	regulation of cAMP/PKA signal transduction
E	1900242	biological_process	regulation of synaptic vesicle endocytosis
E	1900244	biological_process	positive regulation of synaptic vesicle endocytosis
E	1901030	biological_process	positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway
E	1902236	biological_process	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
E	1902499	biological_process	positive regulation of protein autoubiquitination
E	1902531	biological_process	regulation of intracellular signal transduction
E	1902692	biological_process	regulation of neuroblast proliferation
E	1902803	biological_process	regulation of synaptic vesicle transport
E	1902823	biological_process	negative regulation of late endosome to lysosome transport
E	1902902	biological_process	negative regulation of autophagosome assembly
E	1903215	biological_process	negative regulation of protein targeting to mitochondrion
E	1903217	biological_process	negative regulation of protein processing involved in protein targeting to mitochondrion
E	1903351	biological_process	cellular response to dopamine
E	1903980	biological_process	positive regulation of microglial cell activation
E	1904644	biological_process	cellular response to curcumin
E	1904713	molecular_function	beta-catenin destruction complex binding
E	1904887	biological_process	Wnt signalosome assembly
E	1905279	biological_process	regulation of retrograde transport, endosome to Golgi
E	1905289	biological_process	regulation of CAMKK-AMPK signaling cascade
E	1905504	biological_process	negative regulation of motile cilium assembly
E	1990904	cellular_component	ribonucleoprotein complex
E	1990909	cellular_component	Wnt signalosome
E	2000172	biological_process	regulation of branching morphogenesis of a nerve
E	2000300	biological_process	regulation of synaptic vesicle exocytosis
E	2000377	biological_process	regulation of reactive oxygen species metabolic process

Functional Information from PROSITE/UniProt

site_id	PS00107
Number of Residues	22
Details	PROTEIN_KINASE_ATP Protein kinases ATP-binding region signature. LGDGSFGSVYrAayegee............VAVK

Chain	Residue	Details
E	LEU1885-LYS1906

---

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

Chain	Residue	Details
E	ILE1990-LEU2002

---

site_id	PS00626
Number of Residues	11
Details	RCC1_2 Regulator of chromosome condensation (RCC1) signature 2. IGTGgGHILLL

Chain	Residue	Details
E	ILE2427-LEU2437

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Motif: {"description":"Effector region","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	9
Details	Binding site: {"evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	Site: {"description":"Cleavage; by S.typhimurium viral protease GtgE"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by LRRK2","evidences":[{"source":"PubMed","id":"29212815","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; by LRRK2","evidences":[{"source":"PubMed","id":"29212815","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	21
Details	Repeat: {"description":"LRR 1","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	21
Details	Repeat: {"description":"LRR 2","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	21
Details	Repeat: {"description":"LRR 3","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	21
Details	Repeat: {"description":"LRR 4","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	21
Details	Repeat: {"description":"LRR 5","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	21
Details	Repeat: {"description":"LRR 6","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	20
Details	Repeat: {"description":"LRR 7","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	15
Details	Repeat: {"description":"LRR 8","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	22
Details	Repeat: {"description":"LRR 9","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	21
Details	Repeat: {"description":"LRR 10","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	24
Details	Repeat: {"description":"LRR 11","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	21
Details	Repeat: {"description":"LRR 12","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	22
Details	Repeat: {"description":"LRR 13","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	40
Details	Repeat: {"description":"WD 2","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	46
Details	Repeat: {"description":"WD 4","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI21
Number of Residues	44
Details	Repeat: {"description":"WD 5","evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	1
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU00159","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10027","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI23
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00758","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"18230735","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI24
Number of Residues	9
Details	Binding site: {"evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI25
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI26
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8FO2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8FO8","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI27
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00159","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI28
Number of Residues	26
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00758","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI29
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; by autocatalysis","evidences":[{"source":"PubMed","id":"29212815","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30635421","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38127736","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI30
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"28202711","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---