9ZEB | pdb_00009zeb

Cryo-EM structure of the TREX-2.1 complex (Thp3/Csn12/Sem1) bound to the DEAD-box ATPase Sub2

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)
C	SCOP2B Superfamily	DSS1/SEM1 protein family	8053395	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
D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Cop9 signalosome complex subunit 12	DNA binding double-stranded DNA binding binding nucleic acid binding RNA binding	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing cellular response to stimulus cellular response to chemical stimulus response to stimulus response to chemical response to pheromone cellular response to pheromone sexual reproduction reproductive process conjugation with cellular fusion regulation of biological process regulation of cellular process regulation of protein modification process regulation of post-translational protein modification regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of protein neddylation macromolecule modification protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process post-translational protein modification regulation of metabolic process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex COP9 signalosome intracellular organelle cellular anatomical structure intracellular anatomical structure organelle euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex COP9 signalosome intracellular membrane-bounded organelle cytoplasm
C	26S proteasome complex subunit SEM1	molecular adaptor activity protein folding chaperone	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process chromosome organization DNA metabolic process maintenance of DNA repeat elements catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process chromosome organization DNA metabolic process maintenance of DNA repeat elements nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process organelle organization cellular component organization or biogenesis maintenance of DNA trinucleotide repeats cellular response to stimulus double-strand break repair response to stimulus DNA recombination cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair growth filamentous growth SAGA complex localization to transcription regulatory region localization macromolecule localization protein-containing complex localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA 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 cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly regulation of biological process regulation of cellular process biological regulation cell cycle regulation of cell cycle positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary 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 regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic 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 regulation of metabolic process proteasomal protein catabolic process proteasome-mediated 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 organelle nucleus 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 organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transcription export complex 2 proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome accessory complex membraneless organelle intracellular membraneless organelle proteasome storage granule
D	ATP-dependent RNA helicase SUB2	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 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 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 ATP-dependent 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 ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity RNA binding nucleic acid binding	mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process 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 regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process RNA splicing RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 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 establishment of localization RNA export from nucleus establishment of RNA localization macromolecule localization ribonucleoprotein complex biogenesis protein-RNA complex assembly spliceosomal complex assembly protein-RNA complex organization protein-containing complex assembly protein-containing complex organization U2-type prespliceosome assembly transcription elongation by RNA polymerase II DNA-templated transcription DNA-templated transcription elongation transcription by RNA polymerase II cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair	membrane-bounded organelle intracellular organelle protein-containing complex transcription export complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cytoplasm membraneless organelle intracellular membraneless organelle chromosome membrane-bounded organelle intracellular organelle protein-containing complex transcription export complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cytoplasm membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
A	Protein THP3	-	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR045114	Csn12 family	Family
B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B	IPR000717	Proteasome component (PCI) domain	Domain
C	IPR007834	DSS1/SEM1	Family
D	IPR001650	Helicase, C-terminal domain-like	Domain
D	IPR014014	RNA helicase, DEAD-box type, Q motif	Conserved Site
D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
D	IPR011545	DEAD/DEAH-box helicase domain	Domain
D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR000717	Proteasome component (PCI) domain	Domain
A	IPR045107	SAC3/GANP/THP3	Family
A	IPR005062	SAC3/GANP/THP3, conserved domain	Domain