2NZ4 | pdb_00002nz4

Structural investigation of the GlmS ribozyme bound to its catalytic cofactor

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
I [auth A]	d2nz4a_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Splicesomal U1A protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K [auth C]	d2nz4c_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Splicesomal U1A protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L [auth D]	d2nz4d_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Splicesomal U1A protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J [auth B]	d2nz4b_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Splicesomal U1A protein	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)
I [auth A]	SCOP2B Superfamily	RNA-binding domain, RBD	8043930	3000110	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	RNA-binding domain, RBD	8043930	3000110	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	RNA-binding domain, RBD	8043930	3000110	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	RNA-binding domain, RBD	8043930	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)
I [auth A]	Nup35_RRM	e2nz4A1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Nup35_RRM	ECOD (develop294)
K [auth C]	Nup35_RRM	e2nz4C1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Nup35_RRM	ECOD (develop294)
L [auth D]	Nup35_RRM	e2nz4D1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Nup35_RRM	ECOD (develop294)
J [auth B]	Nup35_RRM	e2nz4B1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Nup35_RRM	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth A]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
K [auth C]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
L [auth D]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
J [auth B]	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
I [auth A], J [auth B], K [auth C], L [auth D]	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
I [auth A], J [auth B], K [auth C], L [auth D]	U1 Small Nuclear Ribonucleoprotein A	DNA binding binding nucleic acid binding U1 snRNP binding ribonucleoprotein complex binding snRNP binding protein-containing complex binding RNA binding snRNA binding U1 snRNA binding identical protein binding protein 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	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 spliceosomal snRNP complex Sm-like protein family complex U4/U6 x U5 tri-snRNP complex 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 spliceosomal snRNP complex Sm-like protein family complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex small nuclear ribonucleoprotein complex U1 snRNP membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B [auth P], D [auth Q], F [auth R], H [auth S]	GlmS ribozyme	-	-	-
A [auth E], C [auth F], E [auth G], G [auth H]	substrate strand RNA 13-mer	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth A], J [auth B], K [auth C], L [auth D]	IPR000504	RNA recognition motif domain	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR034407	U1 small nuclear ribonucleoprotein A, RNA recognition motif 1	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR034409	U1 small nuclear ribonucleoprotein A, RNA recognition motif 2	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth A], J [auth B], K [auth C], L [auth D]	Pharos: P09012	lung adenocarcinoma astrocytic tumor hydrolethalus syndrome lung cancer medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor large cell medulloblastoma lung carcinoma mucocutaneous lymph node syndrome ovarian cancer primitive neuroectodermal tumor chronic obstructive pulmonary disease malignant ependymoma lung adenocarcinoma astrocytic tumor hydrolethalus syndrome lung cancer medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor large cell medulloblastoma lung carcinoma mucocutaneous lymph node syndrome ovarian cancer primitive neuroectodermal tumor chronic obstructive pulmonary disease malignant ependymoma nicotine dependence pancreatic ductal adenocarcinoma squamous cell lung carcinoma

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.