6HGC | pdb_00006hgc

Structure of Calypso in complex with DEUBAD of ASX

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2 Family	Asx homology domain-like	8091999	4007762	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	Deubiquitinase adaptor domain (DEUBAD)-like	8092000	3002549	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth B]	DEAD	e6hgcB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: DEAD	ECOD (v294.1)
B [auth C]	DEAD	e6hgcC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: DEAD	ECOD (v294.1)
A	DEAD	e6hgcA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: DEAD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	3.40.532.10	Alpha Beta	3-Layer(aba) Sandwich	Ubiquitin C-terminal Hydrolase UCH-l3	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	CATH (utative)
A	3.40.532.10	Alpha Beta	3-Layer(aba) Sandwich	Ubiquitin C-terminal Hydrolase UCH-l3	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B]	PF18031	Ubiquitin carboxyl-terminal hydrolases (UCH_C)	Ubiquitin carboxyl-terminal hydrolases	This is the C-terminal domain found in eukaryotic UCH37 proteins (also known as Ubiquitin carboxyl-terminal hydrolase isozyme L5, UCHL5). UCH37 is a subunit of two complexes: INO80, which performs ATP-dependent sliding of nucleosomes for transcriptio ...	This is the C-terminal domain found in eukaryotic UCH37 proteins (also known as Ubiquitin carboxyl-terminal hydrolase isozyme L5, UCHL5). UCH37 is a subunit of two complexes: INO80, which performs ATP-dependent sliding of nucleosomes for transcriptional regulation and DNA repair, and the 26S proteasome, which performs ATP-dependent proteolysis of polyubiquitylated proteins in the cytosol and nucleus. Recruitment to the proteasome is mediated by the C-terminal domain of RPN13 (also known as ADRM1). Recruitment to INO80 is mediated by the N-terminal domain of NFRKB. Structural and biochemical analysis reveal that RPN13 and NFRKB make similar interactions with the UCH37 C-terminal domain but have very different interactions with the catalytic UCH domain that are activating in the case of RPN13 and highly inhibitory in the case of NFRKB [3].	Domain
C [auth B]	PF01088	Ubiquitin carboxyl-terminal hydrolase, family 1 (Peptidase_C12)	Ubiquitin carboxyl-terminal hydrolase, family 1		Domain
B [auth C]	PF13919	Asx homology domain (ASXH)	Asx homology domain	A conserved alpha helical domain with a characteristic LXXLL motif [1] [2]. The LXXLL motif is detected in diverse transcription factors, coactivators and corepressors and is implicated in mediating interactions between them [3]. The ASXH domain is ...	A conserved alpha helical domain with a characteristic LXXLL motif [1] [2]. The LXXLL motif is detected in diverse transcription factors, coactivators and corepressors and is implicated in mediating interactions between them [3]. The ASXH domain is found in animals, fungi and plants [4] and is predicted to play a role in mediating contact between transcription factors and chromatin-associated complexes. In Drosophila Asx and Human ASXL1, the ASXH domain is predicted to mediate interactions with the Calypso and BAP1 deubiquitinases (DUBs) which further belong to the UCHL5/UCH37 clade of DUBs [4].	Domain
A	PF18031	Ubiquitin carboxyl-terminal hydrolases (UCH_C)	Ubiquitin carboxyl-terminal hydrolases	This is the C-terminal domain found in eukaryotic UCH37 proteins (also known as Ubiquitin carboxyl-terminal hydrolase isozyme L5, UCHL5). UCH37 is a subunit of two complexes: INO80, which performs ATP-dependent sliding of nucleosomes for transcriptio ...	This is the C-terminal domain found in eukaryotic UCH37 proteins (also known as Ubiquitin carboxyl-terminal hydrolase isozyme L5, UCHL5). UCH37 is a subunit of two complexes: INO80, which performs ATP-dependent sliding of nucleosomes for transcriptional regulation and DNA repair, and the 26S proteasome, which performs ATP-dependent proteolysis of polyubiquitylated proteins in the cytosol and nucleus. Recruitment to the proteasome is mediated by the C-terminal domain of RPN13 (also known as ADRM1). Recruitment to INO80 is mediated by the N-terminal domain of NFRKB. Structural and biochemical analysis reveal that RPN13 and NFRKB make similar interactions with the UCH37 C-terminal domain but have very different interactions with the catalytic UCH domain that are activating in the case of RPN13 and highly inhibitory in the case of NFRKB [3].	Domain
A	PF01088	Ubiquitin carboxyl-terminal hydrolase, family 1 (Peptidase_C12)	Ubiquitin carboxyl-terminal hydrolase, family 1		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B]	Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity chromatin binding binding	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 cellular process negative regulation of biological process cellular component organization 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 cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process developmental process multicellular organismal process blastoderm segmentation embryonic pattern specification specification of segmental identity, abdomen segmentation pattern specification process embryo development regionalization specification of segmental identity, trunk multicellular organism development anatomical structure development trunk segmentation segment specification	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex intracellular organelle cellular anatomical structure organelle PR-DUB complex cytoplasm membraneless organelle intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex intracellular organelle cellular anatomical structure organelle PR-DUB complex cytoplasm membraneless organelle intracellular membraneless organelle chromatin chromosome
B [auth C]	Polycomb protein Asx	DNA binding binding nucleic acid binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity deubiquitinase activator activity peptidase activator activity chromatin binding cation binding transition metal ion binding zinc ion binding DNA binding binding nucleic acid binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity deubiquitinase activator activity peptidase activator activity chromatin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process multicellular organism development multicellular organismal process anterior/posterior axis specification anatomical structure development anterior/posterior pattern specification pattern specification process axis specification regionalization regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process developmental process multicellular organism development multicellular organismal process anterior/posterior axis specification anatomical structure development anterior/posterior pattern specification pattern specification process axis specification regionalization regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular developmental process cell differentiation cell fate determination cell fate commitment imaginal disc morphogenesis imaginal disc-derived wing morphogenesis metamorphosis wing disc morphogenesis imaginal disc development instar larval or pupal morphogenesis post-embryonic animal morphogenesis post-embryonic development animal organ morphogenesis imaginal disc-derived wing margin morphogenesis apposition of dorsal and ventral imaginal disc-derived wing surfaces appendage development post-embryonic appendage morphogenesis animal organ development wing disc development instar larval or pupal development imaginal disc-derived appendage morphogenesis anatomical structure morphogenesis appendage morphogenesis imaginal disc-derived appendage development syncytial blastoderm mitotic cell cycle embryo development mitotic cell cycle mitotic cell cycle, embryonic cell cycle cell cycle comprising mitosis without cytokinesis antennal development eye-antennal disc development positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process epigenetic regulation of gene expression cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis transcription by RNA polymerase II regulation of transcription by RNA polymerase II sensory organ development sex comb development positive regulation of transcription by RNA polymerase II	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex intracellular organelle cellular anatomical structure organelle PR-DUB complex membraneless organelle intracellular membraneless organelle chromatin membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex intracellular organelle cellular anatomical structure organelle PR-DUB complex membraneless organelle intracellular membraneless organelle chromatin chromosome
A	Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity chromatin binding binding	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 cellular process negative regulation of biological process cellular component organization 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 cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process developmental process multicellular organismal process blastoderm segmentation embryonic pattern specification specification of segmental identity, abdomen segmentation pattern specification process embryo development regionalization specification of segmental identity, trunk multicellular organism development anatomical structure development trunk segmentation segment specification	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex intracellular organelle cellular anatomical structure organelle PR-DUB complex cytoplasm membraneless organelle intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex intracellular organelle cellular anatomical structure organelle PR-DUB complex cytoplasm membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B]	IPR041507	Peptidase C12, C-terminal domain	Domain
C [auth B]	IPR036959	Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily	Homologous Superfamily
C [auth B]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
C [auth B]	IPR001578	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	Domain
B [auth C]	IPR026905	Protein ASX-like, PHD domain	Domain
B [auth C]	IPR024811	Polycomb protein ASX/ASX-like	Family
B [auth C]	IPR044867	DEUBAD domain	Domain
B [auth C]	IPR028020	ASX, DEUBAD domain	Domain
A	IPR041507	Peptidase C12, C-terminal domain	Domain
A	IPR036959	Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily	Homologous Superfamily
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR001578	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	Domain

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.