1RKJ | pdb_00001rkj

Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d1rkja1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Nucleolin	golden hamster (Mesocricetus auratus ) [TaxId: 10036 ],	SCOPe (2.08)
B [auth A]	d1rkja3	Artifacts	Tags	Tags	Tags	N-terminal Tags	golden hamster (Mesocricetus auratus ) [TaxId: 10036 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2B Superfamily	RNA-binding domain, RBD	8035358	3000110	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)
B [auth A]	RRM_1_1	e1rkjA2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_1	ECOD (1.6)
B [auth A]	RRM_1_3	e1rkjA1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth 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
B [auth A]	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
A [auth B]	5'-R(GPGPAPUPGPCPCPUPCPCPCPGPAPGPUPGPCPAPUPCP*C)-3'	-	-	-
B [auth A]	Nucleolin	RNA binding binding nucleic acid binding mRNA binding sequence-specific DNA binding DNA binding telomeric DNA binding	-	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 protein-containing complex ribonucleoprotein complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR050502	Eukaryotic RNA-binding	Family
B [auth A]	IPR034234	Nucleolin, RNA recognition motif 3	Domain
B [auth A]	IPR034233	Nucleolin, RNA recognition motif 2	Domain
B [auth A]	IPR000504	RNA recognition motif domain	Domain
B [auth A]	IPR034230	Nucleolin, RNA recognition motif 1	Domain
B [auth A]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B [auth A]	IPR034235	Nucleolin, RNA recognition motif 4	Domain
B [auth A]	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

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.