3WXG | pdb_00003wxg

Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d3wxgf_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3wxgc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3wxge_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3wxgb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Cysteine proteinases	8090283	3001808	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cysteine proteinases	8090283	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8090283	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8090283	3001808	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)
F	Thymidylat_synt	e3wxgF1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
C	Thymidylat_synt	e3wxgC1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
E	Thymidylat_synt	e3wxgE1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
B	Thymidylat_synt	e3wxgB1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
D	Thymidylat_synt	e3wxgD1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
A	Thymidylat_synt	e3wxgA1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
B, E	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
A, D	PF00443	Ubiquitin carboxyl-terminal hydrolase (UCH)	Ubiquitin carboxyl-terminal hydrolase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure myelin sheath intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle cellular anatomical structure myelin sheath intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, E	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure myelin sheath intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle cellular anatomical structure myelin sheath intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, D	Uncharacterized protein	K63-linked deubiquitinase activity ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity cysteine-type deubiquitinase activity cation binding ion binding binding metal ion binding small molecule binding	regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation cellular process cell cycle regulation of cell cycle mitotic cell cycle cellular response to stimulus response to stimulus signaling regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation cellular process cell cycle regulation of cell cycle mitotic cell cycle cellular response to stimulus response to stimulus signaling regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication regulation of intracellular signal transduction signal transduction intrinsic apoptotic signaling pathway regulation of signaling regulation of apoptotic process cell death apoptotic signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway developmental process anatomical structure development cranial skeletal system development negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of p38MAPK cascade negative regulation of biological process p38MAPK cascade negative regulation of cell communication intracellular signaling cassette negative regulation of cellular process negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction regulation of p38MAPK cascade MAPK cascade negative regulation of MAPK cascade biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of response to stimulus positive regulation of cellular process positive regulation of programmed cell death cell surface receptor signaling pathway positive regulation of extrinsic apoptotic signaling pathway positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway positive regulation of signaling protein deubiquitination protein K63-linked deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal negative regulation of JNK cascade JNK cascade regulation of JNK cascade protein linear deubiquitination multicellular organism development multicellular organismal process anatomical structure morphogenesis central nervous system development nervous system development central nervous system morphogenesis system development Wnt signaling pathway necroptotic process programmed necrotic cell death regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development regulation of multicellular organismal process regulation of non-canonical NF-kappaB signal transduction negative regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction proteolysis	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol cell periphery plasma membrane intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol cell periphery plasma membrane membrane perinuclear region of cytoplasm spindle polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR019954	Ubiquitin conserved site	Conserved Site
C, F	IPR000626	Ubiquitin-like domain	Domain
C, F	IPR019956	Ubiquitin domain	Domain
C, F	IPR050158	Ubiquitin and ubiquitin-like	Family
C, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, E	IPR019954	Ubiquitin conserved site	Conserved Site
B, E	IPR000626	Ubiquitin-like domain	Domain
B, E	IPR019956	Ubiquitin domain	Domain
B, E	IPR050158	Ubiquitin and ubiquitin-like	Family
B, E	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, D	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, D	IPR000938	CAP Gly-rich domain	Domain
A, D	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, D	IPR036859	CAP Gly-rich domain superfamily	Homologous Superfamily
A, D	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A, D	IPR001394	Peptidase C19, 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.