6RR0 | pdb_00006rr0

Crystal structure of the Sir4 H-BRCT domain in complex with Ubp10 pT123 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DBF4	e6rr0A1	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: DBF4	ECOD (1.6)
B	DBF4	e6rr0B1	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: DBF4	ECOD (1.6)
C	DBF4	e6rr0C1	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: DBF4	ECOD (1.6)
D	DBF4	e6rr0D1	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: DBF4	ECOD (1.6)
E	DBF4	e6rr0E1	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: DBF4	ECOD (1.6)
F	DBF4	e6rr0F1	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: DBF4	ECOD (1.6)
G	DBF4	e6rr0G1	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: DBF4	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H, I, J, K, L H, I, J, K, L, M, N	Ubiquitin carboxyl-terminal hydrolase 10	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	regulation of protein stability biological regulation regulation of biological quality subtelomeric heterochromatin formation 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 protein stability biological regulation regulation of biological quality subtelomeric heterochromatin formation 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 heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal proteolysis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol nuclear replication fork nuclear chromosome chromosome replication fork chromosome, telomeric region chromosomal region
A, B, C, D, E A, B, C, D, E, F, G	Regulatory protein SIR4	DNA binding double-stranded DNA binding binding nucleic acid binding molecular adaptor activity protein-containing complex binding chromatin binding nucleosome binding	localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization establishment of protein-containing complex localization to telomere macromolecule localization establishment of localization subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization establishment of protein-containing complex localization to telomere macromolecule localization establishment of localization subtelomeric heterochromatin formation 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 constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process silent mating-type cassette heterochromatin formation cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress DNA repair positive regulation of organelle organization positive regulation of heterochromatin organization regulation of heterochromatin formation regulation of chromatin organization regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process positive regulation of heterochromatin formation positive regulation of chromatin organization positive regulation of cellular process positive regulation of cellular component biogenesis chromosome organization regulation of cellular component biogenesis organelle organization regulation of heterochromatin organization	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle chromatin silencing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle chromatin silencing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H, I, J, K, L H, I, J, K, L, M, N	IPR050164	Ubiquitin carboxyl-terminal hydrolases	Family
H, I, J, K, L H, I, J, K, L, M, N	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
H, I, J, K, L H, I, J, K, L, M, N	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
H, I, J, K, L H, I, J, K, L, M, N	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
H, I, J, K, L H, I, J, K, L, M, N	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR031556	Sir4, SID domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
H, I, J, K, L H, I, J, K, L, M, N	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.