Annotations: 28WY

Cryo-EM structure of the human SAC3D1-PCID2-SEM1 complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	DSS1/SEM1 protein family	8053396	3002183	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF01399	PCI domain (PCI)	PCI domain	This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1].	Domain
A	PF03399	SAC3/GANP family (SAC3_GANP)	SAC3/GANP family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	26S proteasome complex subunit SEM1	protein binding binding ubiquitin binding ubiquitin-like protein binding	biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response response to cytokine defense response to symbiont response to external stimulus response to biotic stimulus response to peptide cellular response to type I interferon response to chemical immune system process defense response to other organism response to stress biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response response to cytokine defense response to symbiont response to external stimulus response to biotic stimulus response to peptide cellular response to type I interferon response to chemical immune system process defense response to other organism response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus response to type I interferon cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization intercellular transport mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport intracellular transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process macromolecule localization cellular process metabolic process macromolecule metabolic process catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule catabolic process cellular component organization cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of catabolic process regulation of primary metabolic process regulation of proteasomal protein catabolic process regulation of metabolic process regulation of protein catabolic process response to oxidative stress positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process	protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle integrator complex organelle protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle integrator complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome accessory complex transport vesicle synapse intracellular vesicle endomembrane system presynapse cytoplasmic vesicle synaptic vesicle cell junction secretory vesicle vesicle exocytic vesicle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B	PCI domain-containing protein 2	DNA binding double-stranded DNA binding binding nucleic acid binding RNA binding	developmental process regulation of biological process negative regulation of hematopoietic progenitor cell differentiation regulation of cellular process regulation of developmental process cellular developmental process hemopoiesis negative regulation of developmental process biological regulation negative regulation of biological process cell development regulation of cell differentiation negative regulation of lymphoid progenitor cell differentiation regulation of lymphoid progenitor cell differentiation cell differentiation developmental process regulation of biological process negative regulation of hematopoietic progenitor cell differentiation regulation of cellular process regulation of developmental process cellular developmental process hemopoiesis negative regulation of developmental process biological regulation negative regulation of biological process cell development regulation of cell differentiation negative regulation of lymphoid progenitor cell differentiation regulation of lymphoid progenitor cell differentiation cell differentiation lymphoid progenitor cell differentiation anatomical structure development negative regulation of cellular process cellular process negative regulation of cell differentiation regulation of hematopoietic progenitor cell differentiation hematopoietic progenitor cell differentiation immune system development multicellular organismal process spleen development animal organ development hematopoietic or lymphoid organ development multicellular organism development immune system process animal gross anatomical part developmental process system development cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization intercellular transport mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport poly(A)+ mRNA export from nucleus intracellular transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process macromolecule localization metabolic process macromolecule metabolic process establishment of protein localization protein transport intracellular protein localization transcription elongation by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II cellular component organization organelle organization chromosome organization cellular component organization or biogenesis transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation positive regulation of B cell differentiation lymphocyte differentiation regulation of cell development positive regulation of developmental process positive regulation of cell activation positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process positive regulation of cell development positive regulation of multicellular organismal process leukocyte differentiation positive regulation of biological process lymphocyte activation leukocyte activation positive regulation of lymphocyte activation regulation of B cell differentiation B cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of B cell activation regulation of multicellular organismal process positive regulation of cellular process regulation of lymphocyte differentiation regulation of multicellular organismal development B cell activation cell activation positive regulation of B cell activation regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process chromatin organization chromatin remodeling negative regulation of macromolecule metabolic process epigenetic regulation of gene expression negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transcription export complex 2 cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transcription export complex 2 cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endomembrane system organelle envelope nuclear envelope nuclear pore nuclear basket nuclear pore
A	Maltose/maltodextrin-binding periplasmic protein,SAC3 domain-containing protein 1	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding	microtubule organizing center organization microtubule cytoskeleton organization cellular component organization centrosome duplication organelle organization centrosome cycle cellular process microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization cell cycle process cell division organelle assembly microtubule organizing center organization microtubule cytoskeleton organization cellular component organization centrosome duplication organelle organization centrosome cycle cellular process microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization cell cycle process cell division organelle assembly membraneless organelle assembly spindle assembly cellular component biogenesis cellular component assembly chromosome segregation spindle organization cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton protein-containing complex centrosome microtubule organizing center membrane-bounded organelle nucleus intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton protein-containing complex centrosome microtubule organizing center membrane-bounded organelle nucleus intracellular membrane-bounded organelle ATPase dependent transmembrane transport complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing extracellular region periplasmic space outer membrane-bounded periplasmic space cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR007834	DSS1/SEM1	Family
B	IPR045114	Csn12 family	Family
B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B	IPR000717	Proteasome component (PCI) domain	Domain
A	IPR000717	Proteasome component (PCI) domain	Domain
A	IPR045107	SAC3/GANP/THP3	Family
A	IPR005062	SAC3/GANP/THP3, conserved domain	Domain
A	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A	IPR006059	Bacterial-type extracellular solute-binding protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	: P60896	squamous cell carcinoma bone disease non-small cell lung carcinoma split hand-foot malformation lung cancer osteoporosis medulloblastoma pneumonia subependymal giant cell astrocytoma
B	: Q5JVF3	acute myeloid leukemia malignant mesothelioma ovarian cancer atrial fibrillation medulloblastoma brain aneurysm osteosarcoma
A	: A6NKF1	melanoma acne cutaneous melanoma lung adenocarcinoma malignant pancreatic neoplasm non-small cell lung carcinoma astrocytic tumor exocrine pancreatic carcinoma lung cancer ovarian cancer breast cancer facioscapulohumeral muscular dystrophy malignant mesothelioma metabolic syndrome X tuberculosis

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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.