7BYF | pdb_00007byf

The crystal structure of mouse ORF10-Rae1-Nup98 complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	EF-hand_1, EF-hand_6, EF-hand_7	e7byfA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)
E [auth D]	V-set	e7byfD1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.1)
B	EF-hand_1, EF-hand_6, EF-hand_7	e7byfB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)
F [auth E]	V-set	e7byfE1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)
E [auth D]	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth D]	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
B, F [auth E]	PF21240	Nup98, Gle2-binding sequence (Nup98_GLEBS)	Nup98, Gle2-binding sequence	This is the Gle2-binding sequence (GLEBS) of Nup98, which forms a hairpin that binds with its C-terminal arm to an essentially invariant hydrophobic surface that extends over the top face of the Rae1 beta-propeller [1]. This interaction is required f ...	This is the Gle2-binding sequence (GLEBS) of Nup98, which forms a hairpin that binds with its C-terminal arm to an essentially invariant hydrophobic surface that extends over the top face of the Rae1 beta-propeller [1]. This interaction is required for Rae1 binding. Rae1-Nup98(GLEBS) form a complex with single-stranded RNA-binding capability that directly binds to the mRNP in several steps of the mRNA export pathway [1-3].	Domain
C [auth F], D [auth C]	PF04797	Herpesvirus dUTPase protein (Herpes_ORF11)	Herpesvirus dUTPase protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E [auth D]	mRNA export factor	protein binding binding ubiquitin binding ubiquitin-like protein binding RNA binding nucleic acid binding	regulation of cytoskeleton organization regulation of cellular component organization regulation of cellular process microtubule cytoskeleton organization regulation of mitotic spindle organization mitotic cell cycle cellular component organization cell cycle cellular component organization or biogenesis regulation of cell cycle microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process regulation of biological process regulation of cytoskeleton organization regulation of cellular component organization regulation of cellular process microtubule cytoskeleton organization regulation of mitotic spindle organization mitotic cell cycle cellular component organization cell cycle cellular component organization or biogenesis regulation of cell cycle microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process regulation of biological process regulation of cell cycle process biological regulation regulation of microtubule-based process regulation of spindle organization regulation of organelle organization mitotic spindle organization organelle organization mitotic cell cycle process cellular process microtubule-based process cytoskeleton organization regulation of microtubule cytoskeleton organization chromosome organization transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery cell division localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport establishment of localization RNA transport nitrogen compound transport nucleic acid transport RNA export from nucleus intercellular transport establishment of RNA localization macromolecule localization RNA localization nuclear export nucleobase-containing compound transport	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen fibrillar center membraneless organelle nuclear lumen mitotic spindle spindle cytoskeleton mitotic spindle pole spindle pole microtubule cytoskeleton protein-containing complex nuclear protein-containing complex nuclear pore cytoplasm nucleoplasm
B, F [auth E]	Peptidase S59 domain-containing protein	molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity transcription coactivator activity transcription regulator activity transcription coregulator activity peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity RNA binding binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity transcription coactivator activity transcription regulator activity transcription coregulator activity peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity RNA binding binding nucleic acid binding nuclear localization sequence binding signal sequence binding peptide binding chromatin binding promoter-specific chromatin binding mRNA binding structural molecule activity structural constituent of nuclear pore	localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization establishment of RNA localization macromolecule localization RNA localization localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport establishment of protein localization cellular localization nucleocytoplasmic transport nuclear transport intracellular transport protein localization to nucleus intercellular transport import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle protein import into nucleus cellular process intracellular protein localization intracellular protein transport RNA export from nucleus nuclear export cellular component organization organelle organization chromosome organization cellular component organization or biogenesis transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery nuclear pore organization protein-containing complex organization pore complex assembly cellular component biogenesis nuclear pore complex assembly nucleus organization cellular component assembly protein-containing complex assembly proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process regulation of cellular process regulation of mRNA splicing, via spliceosome mRNA processing positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process RNA processing regulation of biological process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of mRNA processing regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of mRNA splicing, via spliceosome positive regulation of biological process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular 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 RNA splicing, via transesterification reactions positive regulation of gene expression mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process positive regulation of RNA splicing	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore nuclear membrane membrane organelle membrane membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen nucleoplasm nuclear pore nuclear basket inclusion body nuclear inclusion body ribonucleoprotein complex intracellular membraneless organelle nuclear body membraneless organelle nuclear pore cytoplasmic filaments
C [auth F], D [auth C]	10 protein	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E [auth D]	IPR019775	WD40 repeat, conserved site	Conserved Site
A, E [auth D]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, E [auth D]	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
A, E [auth D]	IPR001680	WD40 repeat	Repeat
A, E [auth D]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B, F [auth E]	IPR037665	Nucleoporin peptidase S59-like	Family
B, F [auth E]	IPR036903	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily	Homologous Superfamily
B, F [auth E]	IPR007230	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain	Domain
B, F [auth E]	IPR021967	Nuclear pore complex protein NUP96, C-terminal domain	Domain
C [auth F], D [auth C]	IPR006882	Herpesvirus Orf11	Family

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.