28XB | pdb_000028xb

Cryo-EM structure of the human UAP56-RNA - LENG8-PCID2-SEM1 complex

External Resource: Annotation

Domain Annotation: SCOP2 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)
D [auth H]	SCOP2B Superfamily	RecA-like P-loop NTPases	8040039	3002019	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth H]	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
D [auth H]	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
C	PF05160	DSS1/SEM1 family (DSS1_SEM1)	DSS1/SEM1 family	-	Family
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
E [auth 1]	RNA (5'-R(PUPUPUPUPUPU)-3')	-	-	-
D [auth H]	Spliceosome RNA helicase DDX39B	RNA binding U6 snRNA binding snRNA binding binding nucleic acid binding U4 snRNA binding protein binding ATP-dependent protein binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding RNA binding U6 snRNA binding snRNA binding binding nucleic acid binding U4 snRNA binding protein binding ATP-dependent protein binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding mRNA binding ATP-dependent activity, acting on RNA ATP-dependent activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity macromolecular conformation isomerase activity identical protein binding	cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization 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 RNA splicing RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process RNA processing ribonucleoprotein complex biogenesis mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle U4 snRNP cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle U4 snRNP cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen U6 snRNP transcription export complex cytoplasm spliceosomal complex
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 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 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,Leukocyte receptor cluster member 8,Leukocyte receptor cluster member 8,Leukocyte receptor cluster member 8,Leukocyte receptor cluster member 8	-	-	protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth H]	IPR014014	RNA helicase, DEAD-box type, Q motif	Conserved Site
D [auth H]	IPR011545	DEAD/DEAH-box helicase domain	Domain
D [auth H]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D [auth H]	IPR001650	Helicase, C-terminal domain-like	Domain
D [auth H]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
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

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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.