5YCA | pdb_00005yca

Crystal structure of inner membrane protein Bqt4 in complex with LEM2

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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	KilA-N	e5ycaA1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: KilA-N	ECOD (1.6)
A	Rad60-SLD	e5ycaA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	Lap-Emerin-Man domain protein 2	chromatin binding binding heterochromatin-nuclear membrane anchor activity protein-membrane adaptor activity chromatin-nuclear membrane anchor activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding double-stranded DNA binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding centromeric DNA binding centromere-nuclear envelope anchor activity	localization chromosome localization organelle localization chromosome attachment to the nuclear envelope cellular process cell cycle subnuclear spatial organization of silent mating-type cassette heterochromatin cell cycle process membrane organization cellular component organization nucleus organization organelle organization nuclear envelope organization nuclear inner membrane organization localization chromosome localization organelle localization chromosome attachment to the nuclear envelope cellular process cell cycle subnuclear spatial organization of silent mating-type cassette heterochromatin cell cycle process membrane organization cellular component organization nucleus organization organelle organization nuclear envelope organization nuclear inner membrane organization cellular component organization or biogenesis endomembrane system organization nuclear membrane organization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization protein localization to heterochromatin intracellular protein localization regulation of cellular process negative regulation of biological process cellular component biogenesis cellular component assembly pericentric heterochromatin organization chromatin organization negative regulation of cellular process chromatin remodeling 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 metabolic process macromolecule metabolic process regulation of metabolic process mitotic nuclear membrane reassembly membrane biogenesis mitotic cell cycle nuclear membrane reassembly mitotic nuclear division organelle fission membrane assembly nuclear division mitotic cell cycle process mitotic nuclear membrane organization attachment of telomeric heterochromatin to nuclear envelope centromere localization protein-containing complex localization centromere clustering at the mitotic interphase nuclear envelope centromere clustering sexual reproduction reproductive process meiotic cell cycle	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system nuclear membrane membrane organelle membrane membrane-enclosed lumen membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system nuclear membrane membrane organelle membrane membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen intracellular membraneless organelle microtubule organizing center cytoskeleton membraneless organelle spindle pole body microtubule cytoskeleton mitotic spindle pole body chromosome, subtelomeric region chromosome chromosome, telomeric region chromosomal region pericentric heterochromatin chromatin heterochromatin chromosome, centromeric region mitotic nuclear bridge midzone mitotic nuclear bridge mitotic nuclear bridge midzone membrane domain chromosome, centromeric core domain CENP-A containing chromatin rDNA heterochromatin organelle inner membrane nuclear inner membrane
A	Ubiquitin-like protein SMT3,Bouquet formation protein 4	DNA binding 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	meiotic chromosome segregation sexual reproduction reproductive process meiotic cell cycle process cellular component organization localization telomere localization meiosis I chromosome localization organelle localization meiotic nuclear division cell cycle cellular component organization or biogenesis chromosome segregation meiotic chromosome segregation sexual reproduction reproductive process meiotic cell cycle process cellular component organization localization telomere localization meiosis I chromosome localization organelle localization 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 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 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 metabolic process macromolecule 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 intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope 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 intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear inner membrane nuclear envelope organelle membrane cytoplasm cell cortex septin ring intracellular membraneless organelle cell periphery cytoskeleton membraneless organelle septin cytoskeleton condensed nuclear chromosome membrane-enclosed lumen nuclear chromosome chromosome intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR025856	HeH/LEM domain	Domain
B [auth C]	IPR041885	MAN1, winged-helix domain	Homologous Superfamily
B [auth C]	IPR044780	Heh2/Src1-like	Family
B [auth C]	IPR018996	Man1/Src1-like, C-terminal	Domain
A	IPR018004	KilA/APSES-type HTH, DNA-binding	Domain
A	IPR036887	HTH APSES-type DNA-binding domain superfamily	Homologous Superfamily
A	IPR037548	Bouquet formation protein 4	Family
A	IPR003163	Transcription regulator HTH, APSES-type DNA-binding domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR000626	Ubiquitin-like domain	Domain
A	IPR022617	Rad60/SUMO-like 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 R01GM157729.