9K1R | pdb_00009k1r

Structure of SF3B core in complex with the intron-U2 snRNA (SF3B-intron-U2 snRNA)

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 [auth A]	SCOP2B Superfamily	WD40 repeat-like	8052534	3001694	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	WD40 repeat-like	8052534	3001694	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	WD40 repeat-like	8051197	3001694	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	WD40 repeat-like	8052535	3001694	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Triquetra zinc finger motif	8051848	3002040	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF10433	RSE1/DDB1/CPSF1 first beta-propeller (Beta-prop_RSE1_1st)	RSE1/DDB1/CPSF1 first beta-propeller	-	Repeat
C [auth A]	PF23726	RSE1/DDB1/CPSF1 second beta-propeller (Beta-prop_RSE1_2nd)	RSE1/DDB1/CPSF1 second beta-propeller	-	Repeat
C [auth A]	PF03178	CPSF A subunit region (CPSF_A)	CPSF A subunit region	-	Repeat
A [auth C]	PF22646	PPP2R1A-like HEAT repeat (PPP2R1A-like_HEAT)	PPP2R1A-like HEAT repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth H]	U2 snRNA	-	-	-
E [auth G]	pre-mRNA intron	-	-	-
D [auth B]	Splicing factor 3B subunit 5	splicing factor binding protein binding binding RNA binding nucleic acid 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 regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process 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 biological process biological regulation regulation of macromolecule 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 regulation of metabolic process ribonucleoprotein complex biogenesis 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 U2-type prespliceosome assembly cellular response to stimulus response to stimulus regulation of cellular response to stress cellular response to stress response to stress regulation of response to stress DNA repair DNA metabolic process regulation of DNA repair DNA damage response regulation of response to stimulus regulation of DNA metabolic process regulation of RNA splicing	membrane-bounded organelle U2-type spliceosomal complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex catalytic complex peptidase complex membrane-bounded organelle U2-type spliceosomal complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex catalytic complex peptidase complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex membraneless organelle protein acetyltransferase complex SAGA-type complex SAGA complex intracellular protein-containing complex precatalytic spliceosome spliceosomal snRNP complex Sm-like protein family complex small nuclear ribonucleoprotein complex U2 snRNP U2-type precatalytic spliceosome U12-type spliceosomal complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C [auth A]	Splicing factor 3B subunit 3	protein-containing complex binding binding RNA binding snRNA binding nucleic acid binding U2 snRNA binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process biosynthetic process RNA splicing, via transesterification reactions U2-type prespliceosome assembly mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process 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 biological process biological regulation regulation of macromolecule 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 regulation of metabolic process catabolic process negative regulation of biological process macromolecule catabolic process negative regulation of protein catabolic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process protein catabolic process regulation of catabolic process regulation of protein catabolic process cellular response to stimulus response to stimulus regulation of cellular response to stress cellular response to stress response to stress regulation of response to stress DNA repair DNA metabolic process regulation of DNA repair DNA damage response regulation of response to stimulus regulation of DNA metabolic process regulation of RNA splicing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen spliceosomal snRNP complex protein-containing complex nuclear protein-containing complex Sm-like protein family complex small nuclear ribonucleoprotein complex ribonucleoprotein complex U2 snRNP catalytic step 2 spliceosome catalytic complex spliceosomal complex nucleoplasm U2-type spliceosomal complex peptidase complex chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex protein acetyltransferase complex SAGA-type complex SAGA complex intracellular protein-containing complex U2-type precatalytic spliceosome precatalytic spliceosome U12-type spliceosomal complex
B [auth D]	PHD finger-like domain-containing protein 5A	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process 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 biological process biological regulation regulation of macromolecule 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 regulation of metabolic process ribonucleoprotein complex biogenesis 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 U2-type prespliceosome assembly developmental process stem cell differentiation cellular developmental process cell differentiation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix U2-type spliceosomal complex protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix U2-type spliceosomal complex protein-containing complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex precatalytic spliceosome intracellular membraneless organelle nuclear speck ribonucleoprotein granule nuclear body nucleoplasm membraneless organelle supramolecular complex nuclear ribonucleoprotein granule spliceosomal snRNP complex Sm-like protein family complex small nuclear ribonucleoprotein complex U2 snRNP U2-type precatalytic spliceosome U12-type spliceosomal complex
A [auth C]	Splicing factor 3B subunit 1	RNA binding binding nucleic acid binding mRNA binding splicing factor binding protein binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process biosynthetic process RNA splicing, via transesterification reactions U2-type prespliceosome assembly mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process transcription by RNA polymerase I positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process regulation of transcription by RNA polymerase I biological regulation regulation of macromolecule 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 regulation of metabolic process positive regulation of transcription by RNA polymerase III transcription by RNA polymerase III regulation of transcription by RNA polymerase III transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II chromatin organization chromatin remodeling	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule spliceosomal snRNP complex protein-containing complex nuclear protein-containing complex Sm-like protein family complex small nuclear ribonucleoprotein complex ribonucleoprotein complex U2 snRNP catalytic step 2 spliceosome catalytic complex spliceosomal complex U11/U12 snRNP U2-type spliceosomal complex U2-type precatalytic spliceosome precatalytic spliceosome U12-type spliceosomal complex ATPase complex B-WICH complex chromatin chromosome SWI/SNF superfamily-type complex prespliceosome U2-type prespliceosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth B]	IPR017089	Splicing factor 3B, subunit 5	Family
D [auth B]	IPR009846	Splicing factor 3B subunit 5/RDS3 complex subunit 10	Family
C [auth A]	IPR050358	RSE1/DDB1/CPSF1	Family
C [auth A]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C [auth A]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
C [auth A]	IPR018846	RSE1/DDB1/CPSF1, first beta-propeller	Domain
C [auth A]	IPR058543	RSE1/DDB1/CPSF1, second beta-propeller	Domain
C [auth A]	IPR004871	RSE1/DDB1/CPSF1, C-terminal	Domain
B [auth D]	IPR005345	PHF5-like	Family
A [auth C]	IPR054573	Phosphatase PP2A regulatory subunit A/Splicing factor 3B subunit 1-like, HEAT repeat	Domain
A [auth C]	IPR016024	Armadillo-type fold	Homologous Superfamily
A [auth C]	IPR011989	Armadillo-like helical	Homologous Superfamily
A [auth C]	IPR015016	Splicing factor 3B subunit 1	Domain
A [auth C]	IPR038737	Splicing factor 3B subunit 1-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth B]	Pharos: Q9BWJ5	diabetes mellitus pancreatic ductal adenocarcinoma glioblastoma Sjogren syndrome ovarian cancer
C [auth A]	Pharos: Q15393	astrocytic tumor Intractable Eczema lung cancer atopic eczema large cell medulloblastoma malignant colon neoplasm atypical teratoid rhabdoid tumor ovarian cancer
B [auth D]	Pharos: Q7RTV0	allergic rhinitis vitiligo Crohn disease osteosarcoma
A [auth C]	Pharos: O75533	B-cell chronic lymphocytic leukemia uveal melanoma myelodysplastic syndrome malignant mesothelioma prostate cancer ocular melanoma ovarian cancer primitive neuroectodermal tumor Prostatic Neoplasms abdominal aortic aneurysm thoracic aortic aneurysm anorexia nervosa autism spectrum disorder brain aneurysm malignant ependymoma B-cell chronic lymphocytic leukemia uveal melanoma myelodysplastic syndrome malignant mesothelioma prostate cancer ocular melanoma ovarian cancer primitive neuroectodermal tumor Prostatic Neoplasms abdominal aortic aneurysm thoracic aortic aneurysm anorexia nervosa autism spectrum disorder brain aneurysm malignant ependymoma medulloblastoma oligodendroglioma pancreatic ductal adenocarcinoma progressive supranuclear palsy psoriasis acute myeloid leukemia astrocytic tumor cancer Gaucher disease large cell medulloblastoma osteosarcoma Pick disease allergic rhinitis atypical teratoid rhabdoid tumor bipolar disorder congenital anemia glioblastoma malignant choroid melanoma

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.