4CQ1 | pdb_00004cq1

Crystal structure of the neuronal isoform of PTB

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4cq1a1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4cq1a2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4cq1b1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4cq1b2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4cq1c1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4cq1c2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4cq1d1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4cq1d2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4cq1e1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4cq1e2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4cq1f1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4cq1f2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d4cq1g1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d4cq1g2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d4cq1h1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d4cq1h2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RRM_1_6	e4cq1A1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
B	RRM_1_6	e4cq1B5	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
C	RRM_1_6	e4cq1C1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
D	RRM_1_6	e4cq1D1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
E	RRM_1_6	e4cq1E1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
F	RRM_1_6	e4cq1F1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
G	RRM_1_6	e4cq1G1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
H	RRM_1_6	e4cq1H1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
B	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
C	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
D	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
E	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
F	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
G	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
H	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, B, C, D, E A, B, C, D, E, F, G, H	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
A, B, C, D, E A, B, C, D, E, F, G, H	PF13893	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) (RRM_5)	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	The RRM motif 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 mo ...	The RRM motif 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.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	POLYPYRIMIDINE TRACT-BINDING PROTEIN 2	RNA binding binding nucleic acid binding mRNA 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 mRNA splice site recognition 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 negative regulation of biological process regulation of primary metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of RNA splicing negative regulation of RNA splicing regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process cell population proliferation regulation of cell population proliferation neural precursor cell proliferation regulation of neural precursor cell proliferation	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR021790	PTBP1-like, RNA recognition motif 2	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000504	RNA recognition motif domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR034799	PTBP2, RNA recognition motif 3	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR034800	PTBP2, RNA recognition motif 4	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006536	HnRNP-L/PTB	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR035002	PTBP2, RNA recognition motif 1	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: Q9UKA9	anorexia nervosa endogenous depression malignant colon neoplasm osteosarcoma psoriasis cystic fibrosis large cell medulloblastoma medulloblastoma Pick disease subependymal giant cell astrocytoma dermatomyositis lung cancer nasopharyngeal carcinoma primitive neuroectodermal tumor tuberculosis

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.