4FXW | pdb_00004fxw

Structure of phosphorylated SF1 complex with U2AF65-UHM domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d4fxwc1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Splicing factor U2AF 65 KDa subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4fxwc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4fxwa1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Splicing factor U2AF 65 KDa subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4fxwa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	SF1 HH domain-like	8045251	4004374	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	SF1 HH domain-like	8089885	3002399	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	SF1 HH domain-like	8089885	3002399	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	SF1-HH	e4fxwD1	A: extended segments	X: Splicing factor 1 N-terminal domain (From Topology)	H: Splicing factor 1 N-terminal domain (From Topology)	T: Splicing factor 1 N-terminal domain	F: SF1-HH	ECOD (1.6)
B	SF1-HH	e4fxwB2	A: extended segments	X: Splicing factor 1 N-terminal domain (From Topology)	H: Splicing factor 1 N-terminal domain (From Topology)	T: Splicing factor 1 N-terminal domain	F: SF1-HH	ECOD (1.6)
C	RRM_1_9	e4fxwC2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
A	RRM_1_9	e4fxwA1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00076	RNA recognition motif (RRM_1)	RNA recognition motif	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Splicing factor 1	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding binding nucleic acid binding mRNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding binding nucleic acid binding mRNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein 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 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 regulation of mRNA splicing, via spliceosome regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of RNA splicing regulation of gene expression regulation of macromolecule biosynthetic process regulation of mRNA metabolic process regulation of metabolic process negative regulation of cell population proliferation cell population proliferation regulation of smooth muscle cell proliferation negative regulation of biological process smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation regulation of cell population proliferation negative regulation of cellular process muscle cell proliferation mRNA splice site recognition mRNA 3'-splice site recognition	membrane-bounded organelle 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 U2AF complex membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle 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 U2AF complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle ribosome
A, C	Splicing factor U2AF 65 kDa subunit	poly-pyrimidine tract binding RNA binding binding nucleic acid binding single-stranded RNA binding molecular function inhibitor activity molecular function regulator activity pre-mRNA binding pre-mRNA 3'-splice site binding protein binding enzyme binding C2H2 zinc finger domain binding protein domain specific binding	regulation of cellular process negative regulation of biological process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing negative regulation of mRNA processing regulation of biological process negative regulation of metabolic process regulation of cellular process negative regulation of biological process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing negative regulation of mRNA processing regulation of biological process negative regulation of metabolic process primary metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of mRNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of mRNA processing RNA splicing biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process negative regulation of RNA splicing RNA splicing, via transesterification reactions negative regulation of biosynthetic process mRNA splicing, via spliceosome cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA 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 positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of gene expression positive regulation of RNA splicing negative regulation of post-translational protein modification regulation of protein modification process regulation of protein ubiquitination protein ubiquitination negative regulation of protein modification process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen protein-containing complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex U2AF complex U2-type spliceosomal complex commitment complex prespliceosome U2-type prespliceosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR032570	Splicing factor 1, helix-hairpin domain	Domain
B, D	IPR004087	K Homology domain	Domain
B, D	IPR047086	Splicing factor 1, helix-hairpin domain superfamily	Homologous Superfamily
B, D	IPR001878	Zinc finger, CCHC-type	Domain
B, D	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
B, D	IPR045071	KH domain-containing BBP-like	Family
B, D	IPR055256	KHDC4/BBP-like, KH-domain type I	Domain
A, C	IPR006529	U2 snRNP auxilliary factor, large subunit, splicing factor	Family
A, C	IPR000504	RNA recognition motif domain	Domain
A, C	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, C	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q15637	melanoma ovarian cancer Pick disease psoriasis astrocytic tumor breast cancer cutaneous melanoma head and neck cancer malignant ependymoma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma attention deficit hyperactivity disorder, inattentive type breast carcinoma melanoma ovarian cancer Pick disease psoriasis astrocytic tumor breast cancer cutaneous melanoma head and neck cancer malignant ependymoma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma attention deficit hyperactivity disorder, inattentive type breast carcinoma glioblastoma interstitial lung disease malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor atypical teratoid rhabdoid tumor chronic obstructive pulmonary disease gout large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma
A, C	Pharos: P26368	astrocytic tumor malignant glioma psoriasis large cell medulloblastoma medulloblastoma lung cancer ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D	MSE	Parent Component: MET
B, D	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
A, C	MSE	Parent Component: MET RESID: AA0037

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.