9DLP | pdb_00009dlp

Cryo-EM structure of human TREX-2 complex bound to DDX39B(UAP56)

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)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8040039	3002019	SCOP2B (2022-06-29)
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
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
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
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 organism development multicellular organismal process spleen development immune system process animal organ development hematopoietic or lymphoid organ development 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 chromatin organization chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process epigenetic regulation of gene expression negative regulation of metabolic process regulation of macromolecule metabolic process regulation of gene expression negative regulation of gene expression 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	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 endomembrane system organelle envelope nuclear envelope 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 endomembrane system organelle envelope nuclear envelope nuclear pore nuclear basket nuclear pore
D	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	-	cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein metabolic process 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 component organization cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle integrator complex organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex 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 membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A	Germinal-center associated nuclear protein	binding nucleic acid binding protein binding histone binding protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity histone acetyltransferase activity acetyltransferase activity histone modifying activity binding nucleic acid binding protein binding histone binding protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity histone acetyltransferase activity acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity chromatin binding histone H3 acetyltransferase activity	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 establishment of protein localization protein transport intracellular protein localization immune system development developmental process production of molecular mediator of immune response multicellular organismal process immunoglobulin production somatic diversification of immune receptors via somatic mutation somatic diversification of immunoglobulins multicellular organism development immune system process anatomical structure development somatic diversification of immune receptors somatic hypermutation of immunoglobulin genes system development poly(A)+ mRNA export from nucleus cellular component organization protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling cellular component organization or biogenesis nucleosome organization	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex nuclear protein-containing complex nuclear pore nuclear basket nuclear pore membraneless organelle intracellular membraneless organelle chromosome transcription export complex 2

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
D	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
D	IPR011545	DEAD/DEAH-box helicase domain	Domain
D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D	IPR001650	Helicase, C-terminal domain-like	Domain
D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
C	IPR007834	DSS1/SEM1	Family
A	IPR034265	MCM3AP, RNA recognition motif	Domain
A	IPR031908	Germinal-centre associated nuclear protein, nucleoporin homology domain	Domain
A	IPR031907	Germinal-centre associated nuclear protein, MCM3AP domain	Domain
A	IPR045107	SAC3/GANP/THP3	Family
A	IPR000717	Proteasome component (PCI) domain	Domain
A	IPR031910	Germinal-centre associated nuclear protein, CID domain	Domain
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A	IPR005062	SAC3/GANP/THP3, conserved domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q5JVF3	acute myeloid leukemia malignant mesothelioma ovarian cancer atrial fibrillation medulloblastoma brain aneurysm osteosarcoma
D	Pharos: Q13838	psoriasis Stevens-Johnson syndrome AIDS cancer Crohn disease herpes zoster hypertensive disorder lung carcinoma myasthenia gravis psoriatic arthritis ulcerative colitis allergic rhinitis carpal tunnel syndrome Dengue hemorrhagic fever HIV infectious disease psoriasis Stevens-Johnson syndrome AIDS cancer Crohn disease herpes zoster hypertensive disorder lung carcinoma myasthenia gravis psoriatic arthritis ulcerative colitis allergic rhinitis carpal tunnel syndrome Dengue hemorrhagic fever HIV infectious disease laryngeal squamous cell carcinoma membranous glomerulonephritis myositis squamous cell lung carcinoma autism spectrum disorder cervical cancer Hashimoto thyroiditis Hodgkins lymphoma liver disease metabolic syndrome X
C	Pharos: P60896	squamous cell carcinoma bone disease non-small cell lung carcinoma split hand-foot malformation lung cancer osteoporosis medulloblastoma pneumonia subependymal giant cell astrocytoma
A	Pharos: O60318	testicular germ cell tumor adenoma Charcot-Marie-Tooth disease glioblastoma malignant ependymoma osteosarcoma testicular cancer atypical teratoid rhabdoid tumor colorectal cancer large cell medulloblastoma malignant glioma ovarian cancer breast carcinoma Gaucher disease malignant colon neoplasm testicular germ cell tumor adenoma Charcot-Marie-Tooth disease glioblastoma malignant ependymoma osteosarcoma testicular cancer atypical teratoid rhabdoid tumor colorectal cancer large cell medulloblastoma malignant glioma ovarian cancer breast carcinoma Gaucher disease malignant colon neoplasm medulloblastoma peripheral neuropathy

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.