7UXH | pdb_00007uxh

cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
GA [auth g]SCOP2B SuperfamilyRoadblock/LC7 domain-like 8040242 3001810 SCOP2B (2022-06-29)
ZSCOP2B SuperfamilyRoadblock/LC7 domain-like 8040242 3001810 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyRoadblock/LC7 domain-like 8040242 3001810 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRoadblock/LC7 domain-like 8040242 3001810 SCOP2B (2022-06-29)
YSCOP2B SuperfamilyRoadblock/LC7 domain-like 8088845 3001810 SCOP2B (2022-06-29)
PSCOP2B SuperfamilyRoadblock/LC7 domain-like 8088845 3001810 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyRoadblock/LC7 domain-like 8088845 3001810 SCOP2B (2022-06-29)
FA [auth f]SCOP2B SuperfamilyRoadblock/LC7 domain-like 8088845 3001810 SCOP2B (2022-06-29)
DA [auth d]SCOP2B SuperfamilyRas-like P-loop GTPases 8093371 3002022 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyRas-like P-loop GTPases 8093371 3002022 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyRas-like P-loop GTPases 8093371 3002022 SCOP2B (2022-06-29)
WSCOP2B SuperfamilyRas-like P-loop GTPases 8093371 3002022 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyRas-like P-loop GTPases 8093372 3002022 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyRoadblock/LC7 domain-like 8093374 3001810 SCOP2B (2022-06-29)
VSCOP2B SuperfamilyRoadblock/LC7 domain-like 8093374 3001810 SCOP2B (2022-06-29)
VSCOP2B SuperfamilyRas-like P-loop GTPases 8093372 3002022 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRas-like P-loop GTPases 8093372 3002022 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRoadblock/LC7 domain-like 8093374 3001810 SCOP2B (2022-06-29)
CA [auth c]SCOP2B SuperfamilyRas-like P-loop GTPases 8093372 3002022 SCOP2B (2022-06-29)
CA [auth c]SCOP2B SuperfamilyRoadblock/LC7 domain-like 8093374 3001810 SCOP2B (2022-06-29)
SSCOP2B SuperfamilyRoadblock/LC7 domain-like 8092495 3001810 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRoadblock/LC7 domain-like 8092495 3001810 SCOP2B (2022-06-29)
IA [auth i]SCOP2B SuperfamilyRoadblock/LC7 domain-like 8092495 3001810 SCOP2B (2022-06-29)
BA [auth b]SCOP2B SuperfamilyRoadblock/LC7 domain-like 8092495 3001810 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyFKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) 8036936 3001600 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyFKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) 8036936 3001600 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AA [auth a]PHe7uxha1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
HA [auth h]PHe7uxhh1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
KPHe7uxhK1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
RPHe7uxhR1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
GA [auth g]PHe7uxhg1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
ZPHe7uxhZ1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
QPHe7uxhQ1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
JPHe7uxhJ1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
YPHe7uxhY1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
PPHe7uxhP1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
IPHe7uxhI1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
FA [auth f]PHe7uxhf1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
DA [auth d]PHe7uxhd1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
GPHe7uxhG1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
NPHe7uxhN1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
WPHe7uxhW1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
MPHe7uxhM1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
VPHe7uxhV1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
FPHe7uxhF1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
CA [auth c]PHe7uxhc1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
UPHe7uxhU1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
EPHe7uxhE1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
BPHe7uxhB1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
DPHe7uxhD1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
SPHe7uxhS1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
LPHe7uxhL1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
IA [auth i]PHe7uxhi1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)
BA [auth b]PHe7uxhb1 A: a/b three-layered sandwichesX: RNase A-likeH: Cytochrome P450T: Cytochrome P450F: PHECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
GA [auth g],
J,
Q,
Z		PF08923Mitogen-activated protein kinase kinase 1 interacting (MAPKK1_Int)Mitogen-activated protein kinase kinase 1 interactingMitogen-activated protein kinase kinase 1 interacting protein is a small subcellular adaptor protein required for MAPK signaling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a tw ...Mitogen-activated protein kinase kinase 1 interacting protein is a small subcellular adaptor protein required for MAPK signaling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer [1].
Domain
GA [auth g],
J,
Q,
Z		PF15951MITF/TFEB/TFEC/TFE3 N-terminus (MITF_TFEB_C_3_N)MITF/TFEB/TFEC/TFE3 N-terminus- Family
FA [auth f],
I,
P,
Y		PF16672Ragulator complex protein LAMTOR5 (LAMTOR5)Ragulator complex protein LAMTOR5Domain
FA [auth f],
I,
P,
Y		PF03259Roadblock/LC7 domain (Robl_LC7)Roadblock/LC7 domainThis family includes proteins that are about 100 amino acids long and have been shown to be related [3]. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is pro ...This family includes proteins that are about 100 amino acids long and have been shown to be related [3]. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions [2]. This family also includes Swiss:Q9Y2Q5 Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus Swiss:Q50883, a protein involved in gliding motility [4]. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.
Domain
DA [auth d],
G,
N,
W		PF04670Gtr1/RagA G protein conserved region (Gtr1_RagA)Gtr1/RagA G protein conserved regionGTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is ...GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B [1,2,3,4].
Domain
DA [auth d],
G,
N,
W		PF08923Mitogen-activated protein kinase kinase 1 interacting (MAPKK1_Int)Mitogen-activated protein kinase kinase 1 interactingMitogen-activated protein kinase kinase 1 interacting protein is a small subcellular adaptor protein required for MAPK signaling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a tw ...Mitogen-activated protein kinase kinase 1 interacting protein is a small subcellular adaptor protein required for MAPK signaling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer [1].
Domain
CA [auth c],
F,
M,
V		PF04670Gtr1/RagA G protein conserved region (Gtr1_RagA)Gtr1/RagA G protein conserved regionGTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is ...GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B [1,2,3,4].
Domain
CA [auth c],
F,
M,
V		PF03259Roadblock/LC7 domain (Robl_LC7)Roadblock/LC7 domainThis family includes proteins that are about 100 amino acids long and have been shown to be related [3]. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is pro ...This family includes proteins that are about 100 amino acids long and have been shown to be related [3]. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions [2]. This family also includes Swiss:Q9Y2Q5 Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus Swiss:Q50883, a protein involved in gliding motility [4]. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.
Domain
E, U
PF14538Raptor N-terminal CASPase like domain (Raptor_N)Raptor N-terminal CASPase like domainThis domain is found at the N-terminus of the Raptor protein. It has been identified to have a CASPase like structure [1]. It conserves the characteristic cys/his dyad of the caspases suggesting it may have a peptidase activity. Domain
E, U
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
E, U
PF02985HEAT repeat (HEAT)HEAT repeat- Repeat
B, D
PF04670Gtr1/RagA G protein conserved region (Gtr1_RagA)Gtr1/RagA G protein conserved regionGTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is ...GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B [1,2,3,4].
Domain
B, D
PF16672Ragulator complex protein LAMTOR5 (LAMTOR5)Ragulator complex protein LAMTOR5Domain
B, D
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
JA [auth j],
T		PF15951MITF/TFEB/TFEC/TFE3 N-terminus (MITF_TFEB_C_3_N)MITF/TFEB/TFEC/TFE3 N-terminus- Family
BA [auth b],
IA [auth i],
L,
S		PF16672Ragulator complex protein LAMTOR5 (LAMTOR5)Ragulator complex protein LAMTOR5Domain
A, C
PF02260FATC domain (FATC)FATC domain- Family
A, C
PF23593Serine/threonine-protein kinase ATR-like, HEAT repeats (HEAT_ATR)Serine/threonine-protein kinase ATR-like, HEAT repeats- Repeat
A, C
PF04670Gtr1/RagA G protein conserved region (Gtr1_RagA)Gtr1/RagA G protein conserved regionGTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is ...GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B [1,2,3,4].
Domain
A, C
PF08771FKBP12-rapamycin binding domain (FRB_dom)FKBP12-rapamycin binding domainThe macrolide antibiotic rapamycin and the cytosol protein FKBP12 can form a complex which specifically inhibits the TORC1 complex, leading to growth arrest. The FKBP12-rapamycin complex interferes with TORC1 function by binding to the FKBP12-rapa ...The macrolide antibiotic rapamycin and the cytosol protein FKBP12 can form a complex which specifically inhibits the TORC1 complex, leading to growth arrest. The FKBP12-rapamycin complex interferes with TORC1 function by binding to the FKBP12-rapamycin binding domain (FRB) of the TOR proteins. This entry represents the FRB domain [1, 2].
Domain
A, C
PF00454Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)Phosphatidylinositol 3- and 4-kinase- Family
A, C
PF11865Serine/threonine-protein kinase mTOR domain (mTOR_dom)Serine/threonine-protein kinase mTOR domain- Repeat
A, C
PF02259FAT domain (FAT)FAT domain- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
AA [auth a],
HA [auth h],
K,
R		Ragulator complex protein LAMTOR4-
GA [auth g],
J,
Q,
Z		Ragulator complex protein LAMTOR3
FA [auth f],
I,
P,
Y		Ragulator complex protein LAMTOR2
EA [auth e],
H,
O,
X		Ragulator complex protein LAMTOR1
DA [auth d],
G,
N,
W		Ras-related GTP-binding protein C
CA [auth c],
F,
M,
V		Ras-related GTP-binding protein A
E, U
Regulatory-associated protein of mTOR
B, D
Target of rapamycin complex subunit LST8
JA [auth j],
T		Transcription factor EB
BA [auth b],
IA [auth i],
L,
S		Ragulator complex protein LAMTOR5-
A, C
Serine/threonine-protein kinase mTOR

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
AA [auth a],
HA [auth h],
K,
R		IPR034601Ragulator complex protein LAMTOR4Family
GA [auth g],
J,
Q,
Z		IPR015019Ragulator complex protein LAMTOR3Family
FA [auth f],
I,
P,
Y		IPR037587Ragulator complex protein LAMTOR2-likeFamily
FA [auth f],
I,
P,
Y		IPR004942Roadblock/LAMTOR2 domainDomain
EA [auth e],
H,
O,
X		IPR028209LAMTOR1/MEH1Family
DA [auth d],
G,
N,
W		IPR006762Gtr1/RagA G proteinFamily
DA [auth d],
G,
N,
W		IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
DA [auth d],
G,
N,
W		IPR039400RagC/DFamily
CA [auth c],
F,
M,
V		IPR039397RagA/BFamily
CA [auth c],
F,
M,
V		IPR006762Gtr1/RagA G proteinFamily
CA [auth c],
F,
M,
V		IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
E, U
IPR016024Armadillo-type foldHomologous Superfamily
E, U
IPR004083Regulatory associated protein of TORFamily
E, U
IPR029347Raptor, N-terminal CASPase-like domainDomain
E, U
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
E, U
IPR000357HEAT repeatRepeat
E, U
IPR011989Armadillo-like helicalHomologous Superfamily
E, U
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
E, U
IPR001680WD40 repeatRepeat
B, D
IPR019775WD40 repeat, conserved siteConserved Site
B, D
IPR011047Quinoprotein alcohol dehydrogenase-like superfamilyHomologous Superfamily
B, D
IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
B, D
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
B, D
IPR001680WD40 repeatRepeat
B, D
IPR037588Target of rapamycin complex subunit LST8Family
JA [auth j],
T		IPR024098Transcription factor EB, bHLHzip domainDomain
JA [auth j],
T		IPR021802MiT/TFE transcription factors, C-terminalDomain
JA [auth j],
T		IPR031867MiT/TFE transcription factors, N-terminalDomain
JA [auth j],
T		IPR011598Myc-type, basic helix-loop-helix (bHLH) domainDomain
JA [auth j],
T		IPR036638Helix-loop-helix DNA-binding domain superfamilyHomologous Superfamily
BA [auth b],
IA [auth i],
L,
S		IPR024135Ragulator complex protein LAMTOR5Family
A, C
IPR016024Armadillo-type foldHomologous Superfamily
A, C
IPR009076FKBP12-rapamycin binding domainDomain
A, C
IPR057564Serine/threonine-protein kinase ATR-like, HEAT repeatsDomain
A, C
IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
A, C
IPR036940Phosphatidylinositol 3-/4-kinase, catalytic domain superfamilyHomologous Superfamily
A, C
IPR014009PIK-related kinase, FAT domainDomain
A, C
IPR026683Serine/threonine-protein kinase TOR, catalytic domainDomain
A, C
IPR003151PIK-related kinase, FATDomain
A, C
IPR036738FKBP12-rapamycin binding domain superfamilyHomologous Superfamily
A, C
IPR003152FATC domainDomain
A, C
IPR024585Serine/threonine-protein kinase mTOR domainDomain
A, C
IPR011989Armadillo-like helicalHomologous Superfamily
A, C
IPR000403Phosphatidylinositol 3-/4-kinase, catalytic domainDomain
A, C
IPR050517DNA Damage Response and Repair KinaseFamily
A, C
IPR018936Phosphatidylinositol 3-/4-kinase, conserved siteConserved Site
A, C
IPR011009Protein kinase-like domain superfamilyHomologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
AA [auth a],
HA [auth h],
K,
R		Pharos:  Q0VGL1
GA [auth g],
J,
Q,
Z		Pharos:  Q9UHA4
FA [auth f],
I,
P,
Y		Pharos:  Q9Y2Q5
EA [auth e],
H,
O,
X		Pharos:  Q6IAA8
DA [auth d],
G,
N,
W		Pharos:  Q9HB90
CA [auth c],
F,
M,
V		Pharos:  Q7L523
E, U
Pharos:  Q8N122
B, D
Pharos:  Q9BVC4
JA [auth j],
T		Pharos:  P19484
BA [auth b],
IA [auth i],
L,
S		Pharos:  O43504
A, C
Pharos:  P42345