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8VH5

Cryo-EM structure of Rab12-LRRK2 complex in the LRRK2 dimer state

Functional Information from GO Data
ChainGOidnamespacecontents
A0000139cellular_componentGolgi membrane
A0000149molecular_functionSNARE binding
A0000165biological_processMAPK cascade
A0000287molecular_functionmagnesium ion binding
A0001934biological_processpositive regulation of protein phosphorylation
A0003779molecular_functionactin binding
A0003924molecular_functionGTPase activity
A0004672molecular_functionprotein kinase activity
A0004674molecular_functionprotein serine/threonine kinase activity
A0004676molecular_function3-phosphoinositide-dependent protein kinase activity
A0004677molecular_functionDNA-dependent protein kinase activity
A0004679molecular_functionAMP-activated protein kinase activity
A0004694molecular_functioneukaryotic translation initiation factor 2alpha kinase activity
A0004706molecular_functionJUN kinase kinase kinase activity
A0004709molecular_functionMAP kinase kinase kinase activity
A0004711molecular_functionribosomal protein S6 kinase activity
A0005096molecular_functionGTPase activator activity
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005525molecular_functionGTP binding
A0005615cellular_componentextracellular space
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005741cellular_componentmitochondrial outer membrane
A0005743cellular_componentmitochondrial inner membrane
A0005759cellular_componentmitochondrial matrix
A0005764cellular_componentlysosome
A0005768cellular_componentendosome
A0005783cellular_componentendoplasmic reticulum
A0005789cellular_componentendoplasmic reticulum membrane
A0005794cellular_componentGolgi apparatus
A0005798cellular_componentGolgi-associated vesicle
A0005802cellular_componenttrans-Golgi network
A0005829cellular_componentcytosol
A0005856cellular_componentcytoskeleton
A0005886cellular_componentplasma membrane
A0005902cellular_componentmicrovillus
A0006338biological_processchromatin remodeling
A0006468biological_processprotein phosphorylation
A0006606biological_processprotein import into nucleus
A0006897biological_processendocytosis
A0006914biological_processautophagy
A0006979biological_processresponse to oxidative stress
A0007005biological_processmitochondrion organization
A0007029biological_processendoplasmic reticulum organization
A0007030biological_processGolgi organization
A0007040biological_processlysosome organization
A0007154biological_processcell communication
A0007254biological_processJNK cascade
A0007266biological_processRho protein signal transduction
A0007283biological_processspermatogenesis
A0007528biological_processneuromuscular junction development
A0008017molecular_functionmicrotubule binding
A0008021cellular_componentsynaptic vesicle
A0008104biological_processprotein localization
A0008340biological_processdetermination of adult lifespan
A0009267biological_processcellular response to starvation
A0009966biological_processregulation of signal transduction
A0010468biological_processregulation of gene expression
A0010506biological_processregulation of autophagy
A0010508biological_processpositive regulation of autophagy
A0010955biological_processnegative regulation of protein processing
A0010977biological_processnegative regulation of neuron projection development
A0014041biological_processregulation of neuron maturation
A0015631molecular_functiontubulin binding
A0016242biological_processnegative regulation of macroautophagy
A0016301molecular_functionkinase activity
A0016310biological_processphosphorylation
A0016787molecular_functionhydrolase activity
A0017075molecular_functionsyntaxin-1 binding
A0018105biological_processpeptidyl-serine phosphorylation
A0018107biological_processpeptidyl-threonine phosphorylation
A0019722biological_processcalcium-mediated signaling
A0021756biological_processstriatum development
A0021772biological_processolfactory bulb development
A0022028biological_processtangential migration from the subventricular zone to the olfactory bulb
A0030154biological_processcell differentiation
A0030159molecular_functionsignaling receptor complex adaptor activity
A0030182biological_processneuron differentiation
A0030276molecular_functionclathrin binding
A0030424cellular_componentaxon
A0030425cellular_componentdendrite
A0030426cellular_componentgrowth cone
A0030672cellular_componentsynaptic vesicle membrane
A0031267molecular_functionsmall GTPase binding
A0031344biological_processregulation of cell projection organization
A0031398biological_processpositive regulation of protein ubiquitination
A0031410cellular_componentcytoplasmic vesicle
A0031647biological_processregulation of protein stability
A0031966cellular_componentmitochondrial membrane
A0032091biological_processnegative regulation of protein binding
A0032092biological_processpositive regulation of protein binding
A0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
A0032473cellular_componentcytoplasmic side of mitochondrial outer membrane
A0032760biological_processpositive regulation of tumor necrosis factor production
A0032839cellular_componentdendrite cytoplasm
A0034211molecular_functionGTP-dependent protein kinase activity
A0034260biological_processnegative regulation of GTPase activity
A0034599biological_processcellular response to oxidative stress
A0034614biological_processcellular response to reactive oxygen species
A0035175molecular_functionhistone H3S10 kinase activity
A0035402molecular_functionhistone H3T11 kinase activity
A0035403molecular_functionhistone H3T6 kinase activity
A0035556biological_processintracellular signal transduction
A0035564biological_processregulation of kidney size
A0035640biological_processexploration behavior
A0035641biological_processlocomotory exploration behavior
A0035751biological_processregulation of lysosomal lumen pH
A0035979molecular_functionhistone H2AXS139 kinase activity
A0036479molecular_functionperoxidase inhibitor activity
A0039706molecular_functionco-receptor binding
A0040012biological_processregulation of locomotion
A0042391biological_processregulation of membrane potential
A0042802molecular_functionidentical protein binding
A0042803molecular_functionprotein homodimerization activity
A0042995cellular_componentcell projection
A0043005cellular_componentneuron projection
A0043025cellular_componentneuronal cell body
A0043068biological_processpositive regulation of programmed cell death
A0043195cellular_componentterminal bouton
A0043204cellular_componentperikaryon
A0043231cellular_componentintracellular membrane-bounded organelle
A0043406biological_processpositive regulation of MAP kinase activity
A0044022molecular_functionhistone H3S28 kinase activity
A0044023molecular_functionhistone H4S1 kinase activity
A0044024molecular_functionhistone H2AS1 kinase activity
A0044025molecular_functionhistone H2BS14 kinase activity
A0044325molecular_functiontransmembrane transporter binding
A0044753cellular_componentamphisome
A0044754cellular_componentautolysosome
A0045121cellular_componentmembrane raft
A0045202cellular_componentsynapse
A0045335cellular_componentphagocytic vesicle
A0045746biological_processnegative regulation of Notch signaling pathway
A0045860biological_processpositive regulation of protein kinase activity
A0046039biological_processGTP metabolic process
A0046777biological_processprotein autophosphorylation
A0048312biological_processintracellular distribution of mitochondria
A0048812biological_processneuron projection morphogenesis
A0051018molecular_functionprotein kinase A binding
A0051646biological_processmitochondrion localization
A0051770biological_processpositive regulation of nitric-oxide synthase biosynthetic process
A0051900biological_processregulation of mitochondrial depolarization
A0051966biological_processregulation of synaptic transmission, glutamatergic
A0060070biological_processcanonical Wnt signaling pathway
A0060079biological_processexcitatory postsynaptic potential
A0060159biological_processregulation of dopamine receptor signaling pathway
A0060161biological_processpositive regulation of dopamine receptor signaling pathway
A0060628biological_processregulation of ER to Golgi vesicle-mediated transport
A0060828biological_processregulation of canonical Wnt signaling pathway
A0061001biological_processregulation of dendritic spine morphogenesis
A0070062cellular_componentextracellular exosome
A0070585biological_processprotein localization to mitochondrion
A0070971cellular_componentendoplasmic reticulum exit site
A0070973biological_processprotein localization to endoplasmic reticulum exit site
A0071287biological_processcellular response to manganese ion
A0071407biological_processcellular response to organic cyclic compound
A0072354molecular_functionhistone H3T3 kinase activity
A0072371molecular_functionhistone H2AS121 kinase activity
A0072518molecular_functionRho-dependent protein serine/threonine kinase activity
A0090140biological_processregulation of mitochondrial fission
A0090263biological_processpositive regulation of canonical Wnt signaling pathway
A0090394biological_processnegative regulation of excitatory postsynaptic potential
A0097487cellular_componentmultivesicular body, internal vesicle
A0098794cellular_componentpostsynapse
A0098978cellular_componentglutamatergic synapse
A0099400cellular_componentcaveola neck
A0099523cellular_componentpresynaptic cytosol
A0106310molecular_functionprotein serine kinase activity
A0140058biological_processneuron projection arborization
A0140823molecular_functionhistone H2BS36 kinase activity
A0140855molecular_functionhistone H3S57 kinase activity
A0140857molecular_functionhistone H3T45 kinase activity
A0141161biological_processregulation of cAMP/PKA signal transduction
A1900242biological_processregulation of synaptic vesicle endocytosis
A1900244biological_processpositive regulation of synaptic vesicle endocytosis
A1902236biological_processnegative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
A1902499biological_processpositive regulation of protein autoubiquitination
A1902692biological_processregulation of neuroblast proliferation
A1902803biological_processregulation of synaptic vesicle transport
A1902823biological_processnegative regulation of late endosome to lysosome transport
A1902902biological_processnegative regulation of autophagosome assembly
A1903125biological_processnegative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation
A1903215biological_processnegative regulation of protein targeting to mitochondrion
A1903217biological_processnegative regulation of protein processing involved in protein targeting to mitochondrion
A1903351biological_processcellular response to dopamine
A1903980biological_processpositive regulation of microglial cell activation
A1904713molecular_functionbeta-catenin destruction complex binding
A1904887biological_processWnt signalosome assembly
A1905279biological_processregulation of retrograde transport, endosome to Golgi
A1905289biological_processregulation of CAMKK-AMPK signaling cascade
A1990244molecular_functionhistone H2AT120 kinase activity
A1990606molecular_functionmembrane scission GTPase motor activity
A1990904cellular_componentribonucleoprotein complex
A1990909cellular_componentWnt signalosome
A2000172biological_processregulation of branching morphogenesis of a nerve
A2000300biological_processregulation of synaptic vesicle exocytosis
A2000377biological_processregulation of reactive oxygen species metabolic process
C0000139cellular_componentGolgi membrane
C0000149molecular_functionSNARE binding
C0000165biological_processMAPK cascade
C0000287molecular_functionmagnesium ion binding
C0001934biological_processpositive regulation of protein phosphorylation
C0003779molecular_functionactin binding
C0003924molecular_functionGTPase activity
C0004672molecular_functionprotein kinase activity
C0004674molecular_functionprotein serine/threonine kinase activity
C0004676molecular_function3-phosphoinositide-dependent protein kinase activity
C0004677molecular_functionDNA-dependent protein kinase activity
C0004679molecular_functionAMP-activated protein kinase activity
C0004694molecular_functioneukaryotic translation initiation factor 2alpha kinase activity
C0004706molecular_functionJUN kinase kinase kinase activity
C0004709molecular_functionMAP kinase kinase kinase activity
C0004711molecular_functionribosomal protein S6 kinase activity
C0005096molecular_functionGTPase activator activity
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005525molecular_functionGTP binding
C0005615cellular_componentextracellular space
C0005737cellular_componentcytoplasm
C0005739cellular_componentmitochondrion
C0005741cellular_componentmitochondrial outer membrane
C0005743cellular_componentmitochondrial inner membrane
C0005759cellular_componentmitochondrial matrix
C0005764cellular_componentlysosome
C0005768cellular_componentendosome
C0005783cellular_componentendoplasmic reticulum
C0005789cellular_componentendoplasmic reticulum membrane
C0005794cellular_componentGolgi apparatus
C0005798cellular_componentGolgi-associated vesicle
C0005802cellular_componenttrans-Golgi network
C0005829cellular_componentcytosol
C0005856cellular_componentcytoskeleton
C0005886cellular_componentplasma membrane
C0005902cellular_componentmicrovillus
C0006338biological_processchromatin remodeling
C0006468biological_processprotein phosphorylation
C0006606biological_processprotein import into nucleus
C0006897biological_processendocytosis
C0006914biological_processautophagy
C0006979biological_processresponse to oxidative stress
C0007005biological_processmitochondrion organization
C0007029biological_processendoplasmic reticulum organization
C0007030biological_processGolgi organization
C0007040biological_processlysosome organization
C0007154biological_processcell communication
C0007254biological_processJNK cascade
C0007266biological_processRho protein signal transduction
C0007283biological_processspermatogenesis
C0007528biological_processneuromuscular junction development
C0008017molecular_functionmicrotubule binding
C0008021cellular_componentsynaptic vesicle
C0008104biological_processprotein localization
C0008340biological_processdetermination of adult lifespan
C0009267biological_processcellular response to starvation
C0009966biological_processregulation of signal transduction
C0010468biological_processregulation of gene expression
C0010506biological_processregulation of autophagy
C0010508biological_processpositive regulation of autophagy
C0010955biological_processnegative regulation of protein processing
C0010977biological_processnegative regulation of neuron projection development
C0014041biological_processregulation of neuron maturation
C0015631molecular_functiontubulin binding
C0016242biological_processnegative regulation of macroautophagy
C0016301molecular_functionkinase activity
C0016310biological_processphosphorylation
C0016787molecular_functionhydrolase activity
C0017075molecular_functionsyntaxin-1 binding
C0018105biological_processpeptidyl-serine phosphorylation
C0018107biological_processpeptidyl-threonine phosphorylation
C0019722biological_processcalcium-mediated signaling
C0021756biological_processstriatum development
C0021772biological_processolfactory bulb development
C0022028biological_processtangential migration from the subventricular zone to the olfactory bulb
C0030154biological_processcell differentiation
C0030159molecular_functionsignaling receptor complex adaptor activity
C0030182biological_processneuron differentiation
C0030276molecular_functionclathrin binding
C0030424cellular_componentaxon
C0030425cellular_componentdendrite
C0030426cellular_componentgrowth cone
C0030672cellular_componentsynaptic vesicle membrane
C0031267molecular_functionsmall GTPase binding
C0031344biological_processregulation of cell projection organization
C0031398biological_processpositive regulation of protein ubiquitination
C0031410cellular_componentcytoplasmic vesicle
C0031647biological_processregulation of protein stability
C0031966cellular_componentmitochondrial membrane
C0032091biological_processnegative regulation of protein binding
C0032092biological_processpositive regulation of protein binding
C0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
C0032473cellular_componentcytoplasmic side of mitochondrial outer membrane
C0032760biological_processpositive regulation of tumor necrosis factor production
C0032839cellular_componentdendrite cytoplasm
C0034211molecular_functionGTP-dependent protein kinase activity
C0034260biological_processnegative regulation of GTPase activity
C0034599biological_processcellular response to oxidative stress
C0034614biological_processcellular response to reactive oxygen species
C0035175molecular_functionhistone H3S10 kinase activity
C0035402molecular_functionhistone H3T11 kinase activity
C0035403molecular_functionhistone H3T6 kinase activity
C0035556biological_processintracellular signal transduction
C0035564biological_processregulation of kidney size
C0035640biological_processexploration behavior
C0035641biological_processlocomotory exploration behavior
C0035751biological_processregulation of lysosomal lumen pH
C0035979molecular_functionhistone H2AXS139 kinase activity
C0036479molecular_functionperoxidase inhibitor activity
C0039706molecular_functionco-receptor binding
C0040012biological_processregulation of locomotion
C0042391biological_processregulation of membrane potential
C0042802molecular_functionidentical protein binding
C0042803molecular_functionprotein homodimerization activity
C0042995cellular_componentcell projection
C0043005cellular_componentneuron projection
C0043025cellular_componentneuronal cell body
C0043068biological_processpositive regulation of programmed cell death
C0043195cellular_componentterminal bouton
C0043204cellular_componentperikaryon
C0043231cellular_componentintracellular membrane-bounded organelle
C0043406biological_processpositive regulation of MAP kinase activity
C0044022molecular_functionhistone H3S28 kinase activity
C0044023molecular_functionhistone H4S1 kinase activity
C0044024molecular_functionhistone H2AS1 kinase activity
C0044025molecular_functionhistone H2BS14 kinase activity
C0044325molecular_functiontransmembrane transporter binding
C0044753cellular_componentamphisome
C0044754cellular_componentautolysosome
C0045121cellular_componentmembrane raft
C0045202cellular_componentsynapse
C0045335cellular_componentphagocytic vesicle
C0045746biological_processnegative regulation of Notch signaling pathway
C0045860biological_processpositive regulation of protein kinase activity
C0046039biological_processGTP metabolic process
C0046777biological_processprotein autophosphorylation
C0048312biological_processintracellular distribution of mitochondria
C0048812biological_processneuron projection morphogenesis
C0051018molecular_functionprotein kinase A binding
C0051646biological_processmitochondrion localization
C0051770biological_processpositive regulation of nitric-oxide synthase biosynthetic process
C0051900biological_processregulation of mitochondrial depolarization
C0051966biological_processregulation of synaptic transmission, glutamatergic
C0060070biological_processcanonical Wnt signaling pathway
C0060079biological_processexcitatory postsynaptic potential
C0060159biological_processregulation of dopamine receptor signaling pathway
C0060161biological_processpositive regulation of dopamine receptor signaling pathway
C0060628biological_processregulation of ER to Golgi vesicle-mediated transport
C0060828biological_processregulation of canonical Wnt signaling pathway
C0061001biological_processregulation of dendritic spine morphogenesis
C0070062cellular_componentextracellular exosome
C0070585biological_processprotein localization to mitochondrion
C0070971cellular_componentendoplasmic reticulum exit site
C0070973biological_processprotein localization to endoplasmic reticulum exit site
C0071287biological_processcellular response to manganese ion
C0071407biological_processcellular response to organic cyclic compound
C0072354molecular_functionhistone H3T3 kinase activity
C0072371molecular_functionhistone H2AS121 kinase activity
C0072518molecular_functionRho-dependent protein serine/threonine kinase activity
C0090140biological_processregulation of mitochondrial fission
C0090263biological_processpositive regulation of canonical Wnt signaling pathway
C0090394biological_processnegative regulation of excitatory postsynaptic potential
C0097487cellular_componentmultivesicular body, internal vesicle
C0098794cellular_componentpostsynapse
C0098978cellular_componentglutamatergic synapse
C0099400cellular_componentcaveola neck
C0099523cellular_componentpresynaptic cytosol
C0106310molecular_functionprotein serine kinase activity
C0140058biological_processneuron projection arborization
C0140823molecular_functionhistone H2BS36 kinase activity
C0140855molecular_functionhistone H3S57 kinase activity
C0140857molecular_functionhistone H3T45 kinase activity
C0141161biological_processregulation of cAMP/PKA signal transduction
C1900242biological_processregulation of synaptic vesicle endocytosis
C1900244biological_processpositive regulation of synaptic vesicle endocytosis
C1902236biological_processnegative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
C1902499biological_processpositive regulation of protein autoubiquitination
C1902692biological_processregulation of neuroblast proliferation
C1902803biological_processregulation of synaptic vesicle transport
C1902823biological_processnegative regulation of late endosome to lysosome transport
C1902902biological_processnegative regulation of autophagosome assembly
C1903125biological_processnegative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation
C1903215biological_processnegative regulation of protein targeting to mitochondrion
C1903217biological_processnegative regulation of protein processing involved in protein targeting to mitochondrion
C1903351biological_processcellular response to dopamine
C1903980biological_processpositive regulation of microglial cell activation
C1904713molecular_functionbeta-catenin destruction complex binding
C1904887biological_processWnt signalosome assembly
C1905279biological_processregulation of retrograde transport, endosome to Golgi
C1905289biological_processregulation of CAMKK-AMPK signaling cascade
C1990244molecular_functionhistone H2AT120 kinase activity
C1990606molecular_functionmembrane scission GTPase motor activity
C1990904cellular_componentribonucleoprotein complex
C1990909cellular_componentWnt signalosome
C2000172biological_processregulation of branching morphogenesis of a nerve
C2000300biological_processregulation of synaptic vesicle exocytosis
C2000377biological_processregulation of reactive oxygen species metabolic process
Functional Information from PROSITE/UniProt
site_idPS00107
Number of Residues22
DetailsPROTEIN_KINASE_ATP Protein kinases ATP-binding region signature. LGDGSFGSVYrAayegee............VAVK
ChainResidueDetails
ALEU1885-LYS1906

site_idPS00108
Number of Residues13
DetailsPROTEIN_KINASE_ST Serine/Threonine protein kinases active-site signature. IiYrDLKphNVLL
ChainResidueDetails
AILE1990-LEU2002

site_idPS00626
Number of Residues11
DetailsRCC1_2 Regulator of chromosome condensation (RCC1) signature 2. IGTGgGHILLL
ChainResidueDetails
AILE2427-LEU2437

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues6
DetailsBINDING:
ChainResidueDetails
BGLY49
BASN155
BALA187
DGLY49
DASN155
DALA187

site_idSWS_FT_FI2
Number of Residues2
DetailsBINDING: BINDING => ECO:0000250
ChainResidueDetails
BASP97
DASP97

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: Phosphoserine; by LRRK2 => ECO:0000269|PubMed:26824392, ECO:0000269|PubMed:29125462, ECO:0007744|PubMed:23186163
ChainResidueDetails
BSER106
DSER106
CLEU1885
CLYS1906

site_idSWS_FT_FI4
Number of Residues4
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00758
ChainResidueDetails
AGLU2098
AASN2295
CGLU2098
CASN2295

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:28202711, ECO:0000269|PubMed:28720718, ECO:0000269|PubMed:29212815
ChainResidueDetails
ASER910
CSER910

site_idSWS_FT_FI6
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:28202711, ECO:0000269|PubMed:28720718, ECO:0000269|PubMed:29127255, ECO:0000269|PubMed:29212815, ECO:0000269|PubMed:30635421
ChainResidueDetails
ASER935
CSER935

site_idSWS_FT_FI7
Number of Residues4
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:28202711, ECO:0000269|PubMed:29212815
ChainResidueDetails
ASER955
ASER973
CSER955
CSER973

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:29212815, ECO:0000269|PubMed:30635421
ChainResidueDetails
ASER1292
CSER1292

site_idSWS_FT_FI9
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:28202711
ChainResidueDetails
ASER1444
CSER1444

227111

PDB entries from 2024-11-06

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