6SXO | pdb_00006sxo

Cryo-EM structure of the human Ebp1-ribosome complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth LY]	SCOP2B Superfamily	Translation proteins SH3-like KOW motif containing domain	8076756	3000334	SCOP2B (2022-06-29)
E [auth LX]	SCOP2B Superfamily	Ribosomal proteins S24e, L23 and L15e	8095967	3000210	SCOP2B (2022-06-29)
C [auth Lk]	SCOP2B Superfamily	Ribosomal L38e protein-like	8053567	3002206	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)
F [auth LY]	Ribosomal_L26	e6sxoLY1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Ribosomal_L26	ECOD (1.6)
E [auth LX]	Ribosomal_L23_3	e6sxoLX1	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal proteins S24e, L23 and L15e (From Topology)	T: Ribosomal proteins S24e, L23 and L15e	F: Ribosomal_L23_3	ECOD (1.6)
D [auth LR]	Ribosomal_L19e_N	e6sxoLR1	A: alpha arrays	X: Ribosomal protein L19 (L19e) N-terminal domain (From Topology)	H: Ribosomal protein L19 (L19e) N-terminal domain (From Topology)	T: Ribosomal protein L19 (L19e) N-terminal domain	F: Ribosomal_L19e_N	ECOD (1.6)
D [auth LR]	Ribosomal_L19e_C	e6sxoLR2	A: alpha bundles	X: Ribosomal protein L19 (L19e) C-terminal domain (From Topology)	H: Ribosomal protein L19 (L19e) C-terminal domain (From Topology)	T: Ribosomal protein L19 (L19e) C-terminal domain	F: Ribosomal_L19e_C	ECOD (1.6)
C [auth Lk]	Ribosomal_L38e	e6sxoLk1	A: a+b two layers	X: SRP9/14-like	H: Signal recognition particle alu RNA binding heterodimer SRP9/14-related (From Topology)	T: Signal recognition particle alu RNA binding heterodimer SRP9/14-related	F: Ribosomal_L38e	ECOD (1.6)
B [auth Lh]	Ribosomal_L29_2	e6sxoLh1	A: alpha bundles	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p) (From Topology)	T: Ribosomal protein L29 (L29p)	F: Ribosomal_L29_2	ECOD (1.6)
A	crvDNA_42K	e6sxoA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: crvDNA_42K	ECOD (1.6)
A	Peptidase_M24	e6sxoA2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: Creatinase/aminopeptidase (From Topology)	T: Creatinase/aminopeptidase	F: Peptidase_M24	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F [auth LY]	PF16906	Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26)	Ribosomal proteins L26 eukaryotic, L24P archaeal	-	Family
F [auth LY]	PF00467	KOW motif (KOW)	KOW motif	-	Family
E [auth LX]	PF00276	Ribosomal protein L23 (Ribosomal_L23)	Ribosomal protein L23	-	Family
D [auth LR]	PF01280	Ribosomal protein L19e, N-terminal domain (Ribosomal_L19e)	Ribosomal protein L19e, N-terminal domain	This domain is found at the N-terminal end of the large ribosomal subunit protein eL19 found in eukaryotes and archaea. This is an helical domain that assumes an orthogonal bundle topology.	Domain
A	PF00557	Metallopeptidase family M24 (Peptidase_M24)	Metallopeptidase family M24	This family contains metallopeptidases. It also contains non-peptidase homologues such as the N terminal domain of Spt16 which is a histone H3-H4 binding module [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth L8]	5.8S ribosomal RNA	-	-	-
G [auth L5]	28S ribosomal RNA including ES27L-B (2839-3265)	-	-	-
F [auth LY]	60S ribosomal protein L26	RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome mRNA 5'-UTR binding mRNA binding	cellular response to stimulus response to light stimulus regulation of cellular process response to stimulus protein biosynthetic process regulation of translation involved in cellular response to UV regulation of primary metabolic process cellular response to environmental stimulus post-transcriptional regulation of gene expression cellular response to light stimulus protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process cellular response to stimulus response to light stimulus regulation of cellular process response to stimulus protein biosynthetic process regulation of translation involved in cellular response to UV regulation of primary metabolic process cellular response to environmental stimulus post-transcriptional regulation of gene expression cellular response to light stimulus protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process cellular response to radiation gene expression translation response to UV macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process response to radiation response to abiotic stimulus macromolecule metabolic process cellular response to abiotic stimulus cellular response to UV regulation of metabolic process cellular response to ionizing radiation response to ionizing radiation cellular response to gamma radiation response to gamma radiation ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing nucleobase-containing compound biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of gene expression positive regulation of cell communication positive regulation of signal transduction regulation of cellular response to stress positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of programmed cell death intracellular signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator cell communication intrinsic apoptotic signaling pathway in response to DNA damage signal transduction intrinsic apoptotic signaling pathway positive regulation of programmed cell death positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of apoptotic process positive regulation of intracellular signal transduction cell death positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator regulation of response to stimulus intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway signaling regulation of intrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator positive regulation of response to stimulus cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator regulation of signaling signal transduction by p53 class mediator positive regulation of apoptotic process apoptotic signaling pathway DNA damage response regulation of cell communication positive regulation of intrinsic apoptotic signaling pathway apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death positive regulation of signaling DNA damage response, signal transduction by p53 class mediator regulation of DNA damage response, signal transduction by p53 class mediator positive regulation of DNA damage response, signal transduction by p53 class mediator signal transduction in response to DNA damage cytoplasmic translation ribosomal large subunit biogenesis	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 membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol nucleoplasm cytosolic ribosome ribosome protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit
E [auth LX]	60S ribosomal protein L23a	cell adhesion molecule binding cadherin binding protein binding binding RNA binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome protein-containing complex binding TORC2 complex binding	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process	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 cytosolic ribosome ribosome cytoplasm cytosol extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit
D [auth LR]	60S ribosomal protein L19	RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction 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 anchoring junction cell junction focal adhesion cell-substrate junction membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle nuclear lumen membrane cytosolic ribosome ribosome cytoplasm cytosol synapse protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit
C [auth Lk]	60S ribosomal protein L38	RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome	developmental process ear morphogenesis embryonic organ morphogenesis middle ear morphogenesis multicellular organismal process ear development sensory organ development embryonic morphogenesis animal organ development embryo development multicellular organism development anatomical structure morphogenesis sensory organ morphogenesis anatomical structure development developmental process ear morphogenesis embryonic organ morphogenesis middle ear morphogenesis multicellular organismal process ear development sensory organ development embryonic morphogenesis animal organ development embryo development multicellular organism development anatomical structure morphogenesis sensory organ morphogenesis anatomical structure development animal organ morphogenesis embryonic organ development primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process ossification system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus skeletal system development system development regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly protein-RNA complex assembly cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly cytosolic ribosome assembly protein-containing complex assembly 90S preribosome assembly cellular component organization or biogenesis ribosome assembly tissue development axial mesoderm development mesoderm development	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction intracellular organelle intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction intracellular organelle intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse asymmetric synapse protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit eukaryotic 80S initiation complex translation initiation complex
B [auth Lh]	60S ribosomal protein L35	RNA binding binding nucleic acid binding mRNA binding structural molecule activity structural constituent of ribosome	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process ribosomal large subunit biogenesis macromolecule biosynthetic process nucleic acid metabolic process maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biosynthetic process cellular process metabolic process macromolecule metabolic process maturation of LSU-rRNA translation protein biosynthetic process cytoplasmic translation protein metabolic process	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 membrane cytosolic ribosome ribosome cytoplasm cytosol protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit
A	Proliferation-associated protein 2G4	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity binding nucleic acid binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding RNA binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis RNA processing rRNA metabolic process regulation of protein metabolic process translation protein biosynthetic process post-transcriptional regulation of gene expression regulation of translation protein metabolic process developmental process regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation positive regulation of cellular process	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 membrane extracellular region extracellular exosome extracellular vesicle extracellular organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex ribonucleoprotein complex lytic vacuole intracellular vesicle cytoplasmic vesicle lumen vacuolar lumen endomembrane system cytoplasmic vesicle lysosome vesicle lumen azurophil granule vacuole secretory granule lumen azurophil granule lumen secretory granule primary lysosome secretory vesicle cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth LY]	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
F [auth LY]	IPR005756	Large ribosomal subunit protein uL24, eukaryota_archaea	Family
F [auth LY]	IPR041988	Large ribosomal subunit protein uL24, KOW domain	Domain
F [auth LY]	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
F [auth LY]	IPR005824	KOW	Domain
F [auth LY]	IPR005825	Large ribosomal subunit protein uL24, conserved site	Conserved Site
E [auth LX]	IPR019985	Large ribosomal subunit protein uL23	Family
E [auth LX]	IPR001014	Large ribosomal subunit protein uL23, conserved site	Conserved Site
E [auth LX]	IPR013025	Large ribosomal subunit protein uL23-like	Family
E [auth LX]	IPR012678	Ribosomal protein uL23/eL15/eS24 core domain superfamily	Homologous Superfamily
E [auth LX]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
E [auth LX]	IPR005633	Large ribosomal subunit protein uL23, N-terminal	Domain
D [auth LR]	IPR039547	Large ribosomal subunit protein eL19	Family
D [auth LR]	IPR023638	Large ribosomal subunit protein eL19, conserved site	Conserved Site
D [auth LR]	IPR033935	Large ribosomal subunit protein eL19, eukaryotic	Domain
D [auth LR]	IPR015972	Large ribosomal subunit protein eL19, domain 1	Homologous Superfamily
D [auth LR]	IPR035970	Large ribosomal subunit protein eL19 superfamily	Homologous Superfamily
D [auth LR]	IPR000196	Large ribosomal subunit protein eL19 domain	Domain
C [auth Lk]	IPR002675	Large ribosomal subunit protein eL38	Family
C [auth Lk]	IPR038464	Large ribosomal subunit protein eL38 superfamily	Homologous Superfamily
B [auth Lh]	IPR036049	Large ribosomal subunit protein uL29 superfamily	Homologous Superfamily
B [auth Lh]	IPR045059	Large ribosomal subunit protein uL29, eukaryota	Family
B [auth Lh]	IPR001854	Large ribosomal subunit protein uL29	Family
B [auth Lh]	IPR018254	Large ribosomal subunit protein uL29, conserved site	Conserved Site
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR047113	Proliferation-associated protein 2G4/ARX1	Family
A	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR018349	Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site	Binding Site
A	IPR036005	Creatinase/aminopeptidase-like	Homologous Superfamily
A	IPR004545	PA2G4 family	Family
A	IPR000994	Peptidase M24	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
F [auth LY]	Pharos: P61254	Diamond-Blackfan anemia Diamond-Blackfan anemia 11 Aase Smith syndrome 2 hematopoietic and lymphoid system neoplasm aplastic anemia inherited aplastic anemia congenital anemia
E [auth LX]	Pharos: P62750	breast carcinoma Parkinson disease breast cancer Mammary Neoplasms
D [auth LR]	Pharos: P84098	congenital anemia MALT lymphoma Cytopenia diabetes mellitus
C [auth Lk]	Pharos: P63173	lymphoplasmacytic lymphoma plasma cell myeloma
B [auth Lh]	Pharos: P42766	Diamond-Blackfan anemia Aase Smith syndrome 2 ovarian cancer plasma cell myeloma brain aneurysm large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm diabetes mellitus lymphoplasmacytic lymphoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia
A	Pharos: Q9UQ80	vitiligo allergic rhinitis asthma Disease Exacerbation gastric cancer hereditary diffuse gastric adenocarcinoma malignant mesothelioma polycystic ovary syndrome alopecia areata attention deficit hyperactivity disorder, inattentive type gastric neoplasm large cell medulloblastoma subependymal giant cell astrocytoma anorexia nervosa cleft lip vitiligo allergic rhinitis asthma Disease Exacerbation gastric cancer hereditary diffuse gastric adenocarcinoma malignant mesothelioma polycystic ovary syndrome alopecia areata attention deficit hyperactivity disorder, inattentive type gastric neoplasm large cell medulloblastoma subependymal giant cell astrocytoma anorexia nervosa cleft lip Emery-Dreifuss muscular dystrophy Hashimoto thyroiditis lung cancer myopathy