5YC2

Crystal structure of inner membrane protein Bqt4 in complex with telomeric protein Rap1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	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)
A	F_UNCLASSIFIED	e5yc2A2	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF11976	e5yc2A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF11976	ECOD (1.6)
C	F_UNCLASSIFIED	e5yc2C2	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF11976	e5yc2C1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF11976	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, D	PF09197	Rap1, DNA-binding (Rap1-DNA-bind)	Rap1, DNA-binding	Members of this family, which are predominantly found in the yeast protein rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACACC region in th ...	Members of this family, which are predominantly found in the yeast protein rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACACC region in the 3' region of the DNA-binding site [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Ubiquitin-like protein SMT3,Bouquet formation protein 4	DNA binding binding organic cyclic compound binding nucleic acid binding telomere-nuclear envelope anchor activity protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein tag activity molecular tag activity protein binding ubiquitin-like protein ligase binding enzyme binding identical protein binding	establishment of organelle localization meiotic chromosome segregation cellular localization sexual reproduction reproductive process meiotic cell cycle process cellular component organization localization telomere localization meiosis I chromosome localization organelle localization establishment of localization in cell meiotic nuclear division establishment of organelle localization meiotic chromosome segregation cellular localization sexual reproduction reproductive process meiotic cell cycle process cellular component organization localization telomere localization meiosis I chromosome localization organelle localization establishment of localization in cell meiotic nuclear division cell cycle cellular component organization or biogenesis chromosome segregation cell cycle process meiotic cell cycle organelle fission meiotic telomere clustering chromosome organization establishment of localization chromosome organization involved in meiotic cell cycle nuclear division organelle organization chromosome localization to nuclear envelope involved in homologous chromosome segregation meiosis I cell cycle process nuclear chromosome segregation cellular process homologous chromosome segregation establishment of chromosome localization telomere organization cell division mitotic telomere clustering and tethering at nuclear periphery telomere tethering at nuclear periphery mitotic telomere tethering at nuclear periphery meiotic telomere tethering at nuclear periphery meiotic attachment of telomere to nuclear envelope chromosome attachment to the nuclear envelope primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process macromolecule metabolic process organonitrogen compound metabolic process peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle protein-containing complex nuclear membrane complex Bqt3-Bqt4 intracellular anatomical structure organelle inner membrane nuclear membrane membrane nucleus membrane protein complex nuclear protein-containing complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle membrane-bounded organelle protein-containing complex nuclear membrane complex Bqt3-Bqt4 intracellular anatomical structure organelle inner membrane nuclear membrane membrane nucleus membrane protein complex nuclear protein-containing complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear inner membrane nuclear envelope organelle membrane cytoplasm cell cortex septin ring cell periphery cytoskeleton intracellular non-membrane-bounded organelle septin cytoskeleton non-membrane-bounded organelle condensed nuclear chromosome membrane-enclosed lumen nuclear chromosome chromosome intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen
B, D	DNA-binding protein rap1	sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding telomeric DNA binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process mitotic telomere clustering and tethering at nuclear periphery localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization mitotic telomere tethering at nuclear periphery cellular response to stimulus telomere maintenance in response to DNA damage response to stimulus telomere organization cellular component organization cellular response to stress response to stress cellular component organization or biogenesis protection from non-homologous end joining at telomere chromosome organization DNA metabolic process telomere maintenance organelle organization telomere capping DNA damage response telomere maintenance via telomere lengthening establishment of organelle localization meiotic attachment of telomeric heterochromatin to spindle pole body meiotic chromosome segregation cellular localization sexual reproduction reproductive process meiotic cell cycle process meiosis I establishment of localization in cell meiotic nuclear division cell cycle chromosome segregation cell cycle process meiotic cell cycle organelle fission meiotic telomere clustering establishment of localization chromosome organization involved in meiotic cell cycle nuclear division chromosome localization to nuclear envelope involved in homologous chromosome segregation meiosis I cell cycle process nuclear chromosome segregation microtubule-based process homologous chromosome segregation establishment of chromosome localization	intracellular anatomical structure meiotic spindle pole body cellular anatomical entity intracellular organelle microtubule organizing center cytoskeleton organelle intracellular non-membrane-bounded organelle spindle pole body microtubule cytoskeleton non-membrane-bounded organelle membrane-bounded organelle protein-containing complex protein-DNA complex intracellular anatomical structure meiotic spindle pole body cellular anatomical entity intracellular organelle microtubule organizing center cytoskeleton organelle intracellular non-membrane-bounded organelle spindle pole body microtubule cytoskeleton non-membrane-bounded organelle membrane-bounded organelle protein-containing complex protein-DNA complex nucleus nuclear protein-containing complex chromosome intracellular membrane-bounded organelle chromosomal region telomere cap complex chromosome, telomeric repeat region chromosome, telomeric region shelterin complex nuclear telomere cap complex nucleus leading edge

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR018004	KilA/APSES-type HTH, DNA-binding	Domain
A, C	IPR036887	HTH APSES-type DNA-binding domain superfamily	Homologous Superfamily
A, C	IPR037548	Bouquet formation protein 4	Family
A, C	IPR003163	Transcription regulator HTH, APSES-type DNA-binding domain	Domain
A, C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C	IPR000626	Ubiquitin-like domain	Domain
A, C	IPR022617	Rad60/SUMO-like domain	Domain
B, D	IPR039595	TE2IP/Rap1	Family
B, D	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
B, D	IPR001357	BRCT domain	Domain
B, D	IPR015280	Rap1, DNA-binding domain	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 R01GM133198.