3MMY | pdb_00003mmy

Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	PBP	e3mmyH1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
F	PBP	e3mmyF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
D	PBP	e3mmyD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
B	Coq4	e3mmyB1	A: a/b three-layered sandwiches	X: Oncogene product-like	H: Repressor of bacterial conjugation FinO	T: Repressor of bacterial conjugation FinO	F: Coq4	ECOD (v294.1)
G	Cupredoxin_1	e3mmyG2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Cupredoxin_1	ECOD (v294.1)
E	PBP	e3mmyE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
C	Cupredoxin_1	e3mmyC2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Cupredoxin_1	ECOD (v294.1)
A	Col-Pyo_DNase	e3mmyA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: DEATH domain	T: DEATH domain	F: Col-Pyo_DNase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.10.2360	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
F	1.10.10.2360	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
D	1.10.10.2360	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
B	1.10.10.2360	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
G	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
E	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	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
A, C, E, G	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Nuclear pore complex protein Nup98	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	cellular component organization nucleus organization organelle organization nuclear pore organization protein-containing complex organization cellular process cellular component organization or biogenesis localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization RNA transport nitrogen compound transport cellular component organization nucleus organization organelle organization nuclear pore organization protein-containing complex organization cellular process cellular component organization or biogenesis 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 cellular localization nucleocytoplasmic transport nuclear transport establishment of localization in cell intracellular transport establishment of protein localization protein localization to nucleus intercellular transport import into nucleus establishment of protein localization to organelle protein transport protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport RNA export from nucleus nuclear export chromosome organization transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery pore complex assembly cellular component biogenesis nuclear pore complex assembly 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 cytoplasm cytosol 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
A, C, E, G	mRNA export factor	cytoskeletal protein binding microtubule binding protein binding binding tubulin 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 cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization intercellular transport 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 metabolic process macromolecule metabolic process	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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H	Pharos: P52948	acute myeloid leukemia anemia lymphopenia neutropenia plasma cell myeloma glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma sinusitis Acute Myeloid Leukemia (AML-M2) atypical teratoid rhabdoid tumor Hirschsprung disease, susceptibility to, 1 leukemia malignant mesothelioma acute myeloid leukemia anemia lymphopenia neutropenia plasma cell myeloma glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma sinusitis Acute Myeloid Leukemia (AML-M2) atypical teratoid rhabdoid tumor Hirschsprung disease, susceptibility to, 1 leukemia malignant mesothelioma myopathy ovarian cancer tuberculosis cystic fibrosis invasive ductal breast carcinoma lung cancer
A, C, E, G	Pharos: P78406	colorectal cancer medulloblastoma pancreatic intraductal papillary-mucinous neoplasm dermatomyositis non-small cell lung carcinoma lung cancer osteosarcoma

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.