5Y3A | pdb_00005y3a

Crystal structure of Ragulator complex (p18 49-161)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d5y3ah_	Alpha and beta proteins (a+b)	Profilin-like	Roadblock/LC7 domain	Roadblock/LC7 domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5y3ac_	Alpha and beta proteins (a+b)	Profilin-like	Roadblock/LC7 domain	Roadblock/LC7 domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5y3ag_	Alpha and beta proteins (a+b)	Profilin-like	Roadblock/LC7 domain	Roadblock/LC7 domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5y3ab_	Alpha and beta proteins (a+b)	Profilin-like	Roadblock/LC7 domain	Roadblock/LC7 domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	Roadblock/LC7 domain-like	8092495	3001810	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Roadblock/LC7 domain-like	8092495	3001810	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Roadblock/LC7 domain-like	8040242	3001810	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Roadblock/LC7 domain-like	8040242	3001810	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Roadblock/LC7 domain-like	8088845	3001810	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Roadblock/LC7 domain-like	8088845	3001810	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)
J	ATP-synt_VA_C	e5y3aJ1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_VA_C	ECOD (develop294)
E		e5y3aE1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F:	ECOD (develop294)
I	ATP-synt_VA_C	e5y3aI1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_VA_C	ECOD (develop294)
D		e5y3aD1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F:	ECOD (develop294)
H	ATP-synt_VA_C	e5y3aH1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_VA_C	ECOD (develop294)
C		e5y3aC1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F:	ECOD (develop294)
G	ATP-synt_VA_C	e5y3aG1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_VA_C	ECOD (develop294)
B		e5y3aB1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.30.450.30	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Dynein light chain 2a, cytoplasmic	CATH (4.3.0)
E	3.30.450.30	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Dynein light chain 2a, cytoplasmic	CATH (4.3.0)
H	3.30.450.30	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Dynein light chain 2a, cytoplasmic	CATH (4.3.0)
C	3.30.450.30	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Dynein light chain 2a, cytoplasmic	CATH (4.3.0)
G	3.30.450.30	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Dynein light chain 2a, cytoplasmic	CATH (4.3.0)
B	3.30.450.30	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Dynein light chain 2a, cytoplasmic	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, J	PF16672	Ragulator complex protein LAMTOR5 (LAMTOR5)	Ragulator complex protein LAMTOR5		Domain
C, H	PF08923	Mitogen-activated protein kinase kinase 1 interacting (MAPKK1_Int)	Mitogen-activated protein kinase kinase 1 interacting	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 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, J	Ragulator complex protein LAMTOR5	-	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction positive regulation of TORC1 signaling intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction positive regulation of TORC1 signaling intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction regulation of TORC1 signaling positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process TORC1 signaling positive regulation of signaling multicellular organismal process positive regulation of interleukin-8 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of multicellular organismal process regulation of biosynthetic process interleukin-8 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process regulation of interleukin-8 production positive regulation of canonical NF-kappaB signal transduction intracellular signaling cassette canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction regulation of localization regulation of protein localization positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus localization macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical response to amino acid protein localization to lysosome protein localization to vacuole negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death cellular component organization regulation of cellular component size cellular component organization or biogenesis regulation of biological quality regulation of cell size regulation of anatomical structure size viral genome replication viral process viral life cycle biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm organelle membrane lysosome GTPase activator complex protein-containing complex FNIP-folliculin RagC/D GAP enzyme activator complex cytosol Ragulator complex membrane protein complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle
D, I	Ragulator complex protein LAMTOR4	-	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction positive regulation of TORC1 signaling intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction positive regulation of TORC1 signaling intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction regulation of TORC1 signaling positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process TORC1 signaling positive regulation of signaling cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical response to amino acid protein localization to lysosome localization protein localization to organelle macromolecule localization protein localization to vacuole intracellular protein localization cellular component organization regulation of cellular component size cellular component organization or biogenesis regulation of biological quality regulation of cell size regulation of anatomical structure size	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm organelle membrane lysosome Ragulator complex protein-containing complex membrane protein complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle GTPase activator complex FNIP-folliculin RagC/D GAP enzyme activator complex
C, H	Ragulator complex protein LAMTOR3	enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase regulator activity	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction positive regulation of TORC1 signaling intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction positive regulation of TORC1 signaling intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction regulation of TORC1 signaling positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process TORC1 signaling positive regulation of signaling intracellular signaling cassette positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical response to amino acid localization macromolecule localization intracellular protein localization protein localization to cell junction	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane anchoring junction cell junction focal adhesion cell-substrate junction specific granule membrane specific granule vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome GTPase activator complex protein-containing complex FNIP-folliculin RagC/D GAP enzyme activator complex extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle endosome membrane endosome cell periphery plasma membrane Ragulator complex membrane protein complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex late endosome membrane late endosome
B, G	Ragulator complex protein LAMTOR2	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity molecular adaptor activity	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction positive regulation of TORC1 signaling intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction positive regulation of TORC1 signaling intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction regulation of TORC1 signaling positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process TORC1 signaling positive regulation of signaling intracellular signaling cassette positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical response to amino acid cellular component organization cell junction organization regulation of cellular component organization cell-substrate junction organization regulation of cell-substrate junction organization cellular component organization or biogenesis localization macromolecule localization intracellular protein localization protein localization to cell junction regulation of growth growth regulation of cell growth cell growth ameboidal-type cell migration cell migration fibroblast migration cell motility	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule membrane specific granule vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome GTPase activator complex protein-containing complex FNIP-folliculin RagC/D GAP enzyme activator complex endosome membrane endosome cell periphery plasma membrane Ragulator complex membrane protein complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex late endosome late endosome membrane
A, F	Ragulator complex protein LAMTOR1	protein binding binding enzyme binding GTPase binding protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	localization organelle localization lysosome localization vacuolar localization cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular process positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process localization organelle localization lysosome localization vacuolar localization cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular process positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of signaling regulation of growth regulation of cellular component organization growth regulation of cell growth cell growth cellular component organization cellular component organization or biogenesis TORC1 signaling regulation of sterol transport regulation of localization transport regulation of transport lipid localization lipid transport regulation of lipid transport regulation of cholesterol import organic hydroxy compound transport establishment of localization regulation of lipid localization macromolecule localization cholesterol transport sterol transport regulation of cholesterol transport cholesterol import sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis lysosome organization organelle organization vacuole organization lytic vacuole organization positive regulation of TORC1 signaling regulation of TORC1 signaling regulation of protein localization protein localization to vacuole regulation of protein localization to lysosome protein localization to lysosome positive regulation of protein localization to lysosome protein localization to organelle positive regulation of protein localization intracellular protein localization cellular localization establishment of localization in cell intracellular transport vesicle-mediated transport endosomal transport intracellular signaling cassette positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade regulation of cholesterol efflux cholesterol efflux cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical response to amino acid localization within membrane protein localization to membrane regulation of receptor recycling regulation of macromolecule metabolic process receptor recycling receptor metabolic process metabolic process macromolecule metabolic process regulation of metabolic process vesicle organization endosome organization endomembrane system organization	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule GTPase activator complex protein-containing complex FNIP-folliculin RagC/D GAP enzyme activator complex extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle lytic vacuole lysosome vacuolar membrane azurophil granule vacuole lytic vacuole membrane lysosomal membrane primary lysosome azurophil granule membrane cell periphery plasma membrane membrane microdomain membrane raft Ragulator complex membrane protein complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex endosome membrane endosome late endosome membrane late endosome ficolin-1-rich granule membrane ficolin-1-rich granule tertiary granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, J	IPR024135	Ragulator complex protein LAMTOR5	Family
D, I	IPR034601	Ragulator complex protein LAMTOR4	Family
C, H	IPR015019	Ragulator complex protein LAMTOR3	Family
B, G	IPR037587	Ragulator complex protein LAMTOR2-like	Family
B, G	IPR004942	Roadblock/LAMTOR2 domain	Domain
A, F	IPR028209	LAMTOR1/MEH1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, J	Pharos: O43504	breast carcinoma breast cancer lymphoplasmacytic lymphoma Mammary Neoplasms, Human plasma cell myeloma ovarian cancer glucose intolerance pancreatic ductal adenocarcinoma
D, I	Pharos: Q0VGL1	osteosarcoma ovarian cancer psoriasis
C, H	Pharos: Q9UHA4	atypical teratoid rhabdoid tumor interstitial cystitis pancreatic ductal adenocarcinoma psoriasis breast cancer large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm glioblastoma ovarian cancer plasma cell myeloma
B, G	Pharos: Q9Y2Q5	primary immunodeficiency syndrome due to p14 deficiency breast cancer osteosarcoma Sjogren syndrome pancreatic ductal adenocarcinoma tuberculosis
A, F	Pharos: Q6IAA8	malignant pancreatic neoplasm pancreatic ductal adenocarcinoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.