1KOO | pdb_00001koo

THE CRYSTAL STRUCTURE AND MUTATIONAL ANALYSIS OF A NOVEL RNA-BINDING DOMAIN FOUND IN THE HUMAN TAP NUCLEAR MRNA EXPORT FACTOR

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)
B	d1koob_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	mRNA export factor tap	mRNA export factor tap	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1kood_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	mRNA export factor tap	mRNA export factor tap	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1kooc1	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	mRNA export factor tap	mRNA export factor tap	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1kooc2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Non-canonical RBD domain	mRNA export factor tap	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1kooa1	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	mRNA export factor tap	mRNA export factor tap	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1kooa2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Non-canonical RBD domain	mRNA export factor tap	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)
B	SCOP2B Superfamily	L domain-like	8038331	3001010	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	L domain-like	8038331	3001010	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA-binding domain, RBD	8038329	3000110	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L domain-like	8038331	3001010	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L domain-like	8038331	3001010	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8038329	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		e1kooB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Hexapep,Acetyltransf_11	F:	ECOD (20:10:01)
D		e1kooD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Hexapep,Acetyltransf_11	F:	ECOD (20:10:01)
C		e1kooC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
C		e1kooC2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Hexapep,Acetyltransf_11	F:	ECOD (20:10:01)
A		e1kooA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
A		e1kooA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Hexapep,Acetyltransf_11	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
D	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	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)
C	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	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)
A	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF24048	NXF1/2/3/5 leucine-rich repeat domain (LRR_NXF1-5)	NXF1/2/3/5 leucine-rich repeat domain	-	Repeat
A, B, C, D	PF09162	Tap, RNA-binding (Tap-RNA_bind)	Tap, RNA-binding	Members of this family adopt a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. They are mainly found in mRNA export factors, and mediate the sequence nonspecific nuclear export o ...	Members of this family adopt a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. They are mainly found in mRNA export factors, and mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	TIP ASSOCIATING PROTEIN	RNA binding binding nucleic acid binding mRNA binding	cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport intracellular transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process macromolecule localization cellular process metabolic process macromolecule metabolic process establishment of protein localization protein transport intracellular protein localization poly(A)+ mRNA export from nucleus	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule membrane-bounded organelle nucleus membrane-enclosed lumen intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear ribonucleoprotein granule nuclear lumen cytosol protein-containing complex nuclear protein-containing complex endomembrane system organelle envelope nuclear envelope nuclear pore nuclear RNA export factor complex inclusion body nuclear inclusion body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR030217	Nuclear RNA export factor	Family
A, B, C, D	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR015245	Nuclear RNA export factor Tap, RNA-binding domain	Domain
A, B, C, D	IPR057125	NXF1/2/3/5-like, leucine-rich repeat domain	Domain
A, B, C, D	IPR005637	TAP C-terminal (TAP-C) domain	Domain
A, B, C, D	IPR001611	Leucine-rich repeat	Repeat
A, B, C, D	IPR018222	Nuclear transport factor 2, eukaryote	Domain
A, B, C, D	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, B, C, D	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B, C, D	IPR009060	UBA-like superfamily	Homologous Superfamily
A, B, C, D	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR002075	Nuclear transport factor 2 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9UBU9	acute myeloid leukemia

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.