4WWR | pdb_00004wwr

Crystal Structure of Bag6-Ubl4A Dimerization Domain

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H [auth E]	Internalin_N	e4wwrE1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Internalin_N	ECOD (develop294)
F [auth C]	Internalin_N	e4wwrC1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Internalin_N	ECOD (develop294)
D [auth G]	Internalin_N	e4wwrG1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Internalin_N	ECOD (develop294)
B [auth A]	Bag6_BAGS	e4wwrA1	A: alpha bundles	X: Rubredoxin-like	H: Bag6-BAG	T: Bag6-BAG	F: Bag6_BAGS	ECOD (develop294)
G [auth F]	Internalin_N	e4wwrF1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Internalin_N	ECOD (develop294)
E [auth D]	Internalin_N	e4wwrD1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Internalin_N	ECOD (develop294)
C [auth H]	Internalin_N	e4wwrH1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Internalin_N	ECOD (develop294)
A [auth B]	Ank, Ank_2, Ank_3, Ank_4	e4wwrB1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ank, Ank_2, Ank_3, Ank_4	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], D [auth G], F [auth C], H [auth E]	PF20960	Bag6, BAG-similar domain (Bag6_BAGS)	Bag6, BAG-similar domain	Bag6 (BCL2-associated athanogene cochaperone 6) is part of a cytosolic protein quality control complex involved in the post- translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane, in the mislocal ...	Bag6 (BCL2-associated athanogene cochaperone 6) is part of a cytosolic protein quality control complex involved in the post- translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane, in the mislocalised protein degradation pathway and in the endoplasmic reticulum- associated degradation. The BAG-similar domain, found at the C- terminal end of this protein plays a role in the interaction with the other members of the complex, Ubl4A and TRC35. This domain shows three helices in an extended conformation that differ from the three-helix bundle fold of the canonical BAG domain (Pfam:PF02179) [1,2].	Domain
A [auth B], C [auth H], E [auth D], G [auth F]	PF17840	Tethering Ubl4a to BAGS domain (Tugs)	Tethering Ubl4a to BAGS domain	This is the C-terminal domain of Ubiquitin-like protein 4A (Ubl4A), an orthologue of yeast Get5. In budding yeast, GET proteins directly mediate the insertion of newly synthesized TA proteins into endoplasmic reticulum membranes. Similarly, mammalian ...	This is the C-terminal domain of Ubiquitin-like protein 4A (Ubl4A), an orthologue of yeast Get5. In budding yeast, GET proteins directly mediate the insertion of newly synthesized TA proteins into endoplasmic reticulum membranes. Similarly, mammalian BAG6, Ubl4a, and SGTA make up a trimeric complex that binds TA proteins post-translationally and then loads them onto the cytosolic ATPase TRC40, which in turn targets them to the endoplasmic reticulum. Structural studies show that this C-terminal TUGS domain of Ubl4a is essential for BAG6 tethering. Given that BAG6 mediates oligomeric complex formation of Ubl4a, TRC35, and TRC40 (mammalian counterparts of Get5, Get4, and Get3, respectively), the C-terminal TUGS domain might be crucial for supporting BAG6-mediated Ubl4a-TRC35 complex formation in humans as an alternative to the direct Get5-Get4 interaction in yeast [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A], D [auth G], F [auth C], H [auth E]	Large proline-rich protein BAG6	protein binding binding misfolded protein binding protein carrier chaperone molecular carrier activity ubiquitin-specific protease binding enzyme binding protease binding polyubiquitin modification-dependent protein binding modification-dependent protein binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein-containing complex binding protein binding binding misfolded protein binding protein carrier chaperone molecular carrier activity ubiquitin-specific protease binding enzyme binding protease binding polyubiquitin modification-dependent protein binding modification-dependent protein binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein-containing complex binding proteasome binding identical protein binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity Hsp70 protein binding protein-folding chaperone binding heat shock protein binding ribonucleoprotein complex binding ribosome binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress meiotic chromosome segregation synaptonemal complex assembly meiotic cell cycle process cellular component organization cellular component biogenesis cellular component assembly meiosis I meiotic nuclear division cellular component organization or biogenesis cell cycle synaptonemal complex organization chromosome segregation cell cycle process meiotic cell cycle organelle fission chromosome organization chromosome organization involved in meiotic cell cycle organelle organization nuclear division meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation membrane organization establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane tail-anchored membrane protein insertion into ER membrane endoplasmic reticulum organization establishment of localization localization protein localization to organelle macromolecule localization intracellular protein localization protein insertion into membrane protein insertion into ER membrane endomembrane system organization apoptotic process cell death programmed cell death regulation of cellular process negative regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process negative regulation of protein catabolic process modification-dependent macromolecule catabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process regulation of biological process negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process regulation of metabolic process regulation of protein catabolic process immune response-regulating cell surface receptor signaling pathway signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response regulation of response to stimulus immune system process regulation of immune response activation of immune response cell activation natural killer cell activation lymphocyte activation leukocyte activation maintenance of unfolded protein kidney development renal system development chromatin organization cellular developmental process cell differentiation T cell activation alpha-beta T cell activation NK T cell activation negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process tube development respiratory tube development lung development respiratory system development protein targeting post-translational protein targeting to endoplasmic reticulum membrane protein targeting to membrane establishment of protein localization to organelle establishment of protein localization to endoplasmic reticulum protein targeting to ER negative regulation of proteolysis regulation of proteolysis proteolysis endoplasmic reticulum stress-induced pre-emptive quality control intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress intracellular signal transduction apoptotic signaling pathway intrinsic apoptotic signaling pathway signal transduction by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator DNA damage response intrinsic apoptotic signaling pathway by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development regulation of multicellular organismal process peptidyl-lysine acetylation peptidyl-lysine modification protein acylation protein acetylation internal peptidyl-lysine acetylation macromolecule modification peptidyl-amino acid modification protein modification process internal protein amino acid acetylation positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process regulation of cellular response to stress regulation of response to endoplasmic reticulum stress positive regulation of metabolic process positive regulation of response to endoplasmic reticulum stress regulation of response to stress positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of ERAD pathway positive regulation of protein catabolic process positive regulation of catabolic process positive regulation of ERAD pathway	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen protein-containing complex BAT3 complex ER membrane insertion complex
A [auth B], C [auth H], E [auth D], G [auth F]	Ubiquitin-like protein 4A	protein binding binding protein-folding chaperone binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of protein stability biological regulation regulation of biological quality catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of protein stability biological regulation regulation of biological quality macromolecule modification protein modification process membrane organization establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane tail-anchored membrane protein insertion into ER membrane endoplasmic reticulum organization establishment of localization cellular component organization localization organelle organization protein localization to organelle macromolecule localization intracellular protein localization cellular component organization or biogenesis protein insertion into membrane protein insertion into ER membrane endomembrane system organization protein targeting post-translational protein targeting to endoplasmic reticulum membrane protein targeting to membrane establishment of protein localization to organelle establishment of protein localization to endoplasmic reticulum protein targeting to ER	cellular anatomical structure membrane protein-containing complex intracellular anatomical structure BAT3 complex cytoplasm ER membrane insertion complex cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure membrane protein-containing complex intracellular anatomical structure BAT3 complex cytoplasm ER membrane insertion complex cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], D [auth G], F [auth C], H [auth E]	IPR019954	Ubiquitin conserved site	Conserved Site
B [auth A], D [auth G], F [auth C], H [auth E]	IPR000626	Ubiquitin-like domain	Domain
B [auth A], D [auth G], F [auth C], H [auth E]	IPR048926	Bag6, BAG-similar domain	Domain
B [auth A], D [auth G], F [auth C], H [auth E]	IPR021925	Large proline-rich protein BAG6	Domain
B [auth A], D [auth G], F [auth C], H [auth E]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A [auth B], C [auth H], E [auth D], G [auth F]	IPR019954	Ubiquitin conserved site	Conserved Site
A [auth B], C [auth H], E [auth D], G [auth F]	IPR000626	Ubiquitin-like domain	Domain
A [auth B], C [auth H], E [auth D], G [auth F]	IPR019956	Ubiquitin domain	Domain
A [auth B], C [auth H], E [auth D], G [auth F]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A [auth B], C [auth H], E [auth D], G [auth F]	IPR044724	UBL4A-like, ubiquitin-like domain	Domain
A [auth B], C [auth H], E [auth D], G [auth F]	IPR047154	Ubiquitin-like protein 4A-like	Family
A [auth B], C [auth H], E [auth D], G [auth F]	IPR041421	Ubl4, C-terminal TUGS domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A], D [auth G], F [auth C], H [auth E]	Pharos: P46379	rheumatoid arthritis astrocytic tumor Crohn disease hypertensive disorder lung carcinoma membranous glomerulonephritis ovarian cancer squamous cell lung carcinoma autism spectrum disorder cutaneous lupus erythematosus laryngeal squamous cell carcinoma malignant mesothelioma myositis psoriatic arthritis systemic lupus erythematosus rheumatoid arthritis astrocytic tumor Crohn disease hypertensive disorder lung carcinoma membranous glomerulonephritis ovarian cancer squamous cell lung carcinoma autism spectrum disorder cutaneous lupus erythematosus laryngeal squamous cell carcinoma malignant mesothelioma myositis psoriatic arthritis systemic lupus erythematosus cancer Hashimoto thyroiditis lung adenocarcinoma medulloblastoma osteosarcoma
A [auth B], C [auth H], E [auth D], G [auth F]	Pharos: P11441	malignant mesothelioma psoriasis

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.