2QDJ | pdb_00002qdj

Crystal structure of the Retinoblastoma protein N-domain provides insight into tumor suppression, ligand interaction and holoprotein architecture

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Retinoblastoma tumor suppressor protein, N-terminal domain	8047134	4005462	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cyclin-like	8105979	3000768	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cyclin-like	8105978	3000768	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DUF3452	e2qdjA1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: DUF3452	ECOD (1.6)
A	KOG1010	e2qdjA2	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: KOG1010	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.140.1380	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	1.10.472.140	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF11934	Domain of unknown function (DUF3452) (DUF3452)	Domain of unknown function (DUF3452)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Retinoblastoma-associated protein	phosphoprotein binding protein binding binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding identical protein binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding phosphoprotein binding protein binding binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding identical protein binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding kinase binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity importin-alpha family protein binding disordered domain specific binding protein domain specific binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation muscle structure development cellular developmental process cell differentiation anatomical structure development cellular process myoblast differentiation developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation muscle structure development cellular developmental process cell differentiation anatomical structure development cellular process myoblast differentiation cell division multicellular organismal process regulation of cellular process regulation of developmental process negative regulation of biological process cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis negative regulation of glial cell proliferation regulation of cell development regulation of nervous system development neurogenesis multicellular organism development negative regulation of neurogenesis regulation of glial cell proliferation gliogenesis negative regulation of cellular process regulation of multicellular organismal process negative regulation of nervous system development negative regulation of cell differentiation system development regulation of multicellular organismal development regulation of biological process negative regulation of cell population proliferation cell population proliferation negative regulation of developmental process biological regulation nervous system development negative regulation of gliogenesis negative regulation of cell development regulation of cell population proliferation glial cell proliferation negative regulation of multicellular organismal process localization protein localization to chromosome, centromeric region protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization apoptotic process cell death programmed cell death glial cell apoptotic process negative regulation of cell cycle cell cycle regulation of cell cycle attachment of spindle microtubules to kinetochore sister chromatid biorientation chromosome organization sister chromatid segregation cellular component organization metaphase chromosome alignment organelle organization chromosome localization organelle localization nuclear chromosome segregation cellular component organization or biogenesis chromosome segregation cell cycle process regulation of growth regulation of cellular component organization growth negative regulation of cell growth regulation of cell growth cell growth negative regulation of growth regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding positive regulation of transcription regulatory region DNA binding regulation of transcription regulatory region DNA binding positive regulation of binding positive regulation of DNA binding homeostatic process hemopoiesis erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation immune system process homeostasis of number of cells myeloid cell homeostasis enucleate erythrocyte differentiation erythrocyte homeostasis mitotic sister chromatid cohesion sister chromatid cohesion maintenance of sister chromatid cohesion maintenance of mitotic sister chromatid cohesion negative regulation of hepatocyte apoptotic process regulation of epithelial cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death epithelial cell apoptotic process negative regulation of apoptotic process regulation of hepatocyte apoptotic process negative regulation of epithelial cell apoptotic process hepatocyte apoptotic process skeletal muscle cell differentiation skeletal muscle tissue development animal organ development tissue development striated muscle tissue development skeletal muscle organ development muscle tissue development muscle organ development regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of catalytic activity regulation of transferase activity regulation of primary metabolic process negative regulation of kinase activity phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process phosphorus metabolic process protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process negative regulation of molecular function primary metabolic process negative regulation of protein kinase activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of kinase activity negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process metabolic process macromolecule metabolic process negative regulation of phosphorylation regulation of metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription mitotic cell cycle process cell cycle phase transition G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition myeloid leukocyte differentiation regulation of leukocyte differentiation positive regulation of biological process mononuclear cell differentiation positive regulation of developmental process positive regulation of cell differentiation positive regulation of hemopoiesis regulation of immune system process regulation of macrophage differentiation positive regulation of immune system process positive regulation of cellular process regulation of myeloid cell differentiation positive regulation of cell development macrophage differentiation regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation positive regulation of macrophage differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of multicellular organismal process positive regulation of leukocyte differentiation leukocyte differentiation cellular response to stimulus cellular response to chemical stimulus response to stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus striated muscle cell differentiation muscle cell differentiation connective tissue development skeletal system development chondrocyte differentiation cartilage development negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation positive regulation of DNA-templated transcription 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 transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process plasma membrane bounded cell projection organization cell projection organization neuron projection development generation of neurons neuron differentiation neuron development cell surface receptor signaling pathway signaling smoothened signaling pathway cell communication signal transduction negative regulation of DNA-binding transcription factor activity regulation of DNA-binding transcription factor activity regulation of mitotic cell cycle positive regulation of organelle organization regulation of cell cycle phase transition regulation of mitotic nuclear division positive regulation of mitotic nuclear division positive regulation of mitotic metaphase/anaphase transition positive regulation of mitotic cell cycle phase transition mitotic sister chromatid separation regulation of cell cycle process positive regulation of nuclear division regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition regulation of chromosome separation regulation of chromosome segregation regulation of metaphase/anaphase transition of cell cycle regulation of mitotic sister chromatid separation positive regulation of cellular component organization regulation of mitotic metaphase/anaphase transition positive regulation of metaphase/anaphase transition of cell cycle mitotic sister chromatid segregation positive regulation of cell cycle process positive regulation of mitotic cell cycle mitotic nuclear division organelle fission positive regulation of cell cycle nuclear division chromosome separation regulation of sister chromatid segregation positive regulation of cell cycle phase transition positive regulation of mitotic sister chromatid separation regulation of nuclear division metaphase/anaphase transition of mitotic cell cycle positive regulation of chromosome separation metaphase/anaphase transition of cell cycle developmental maturation anatomical structure maturation neuron maturation cell maturation digestive system development tube development digestive tract development regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response negative regulation of signaling regulation of signal transduction negative regulation of cell communication negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway regulation of signaling negative regulation of signal transduction regulation of cell communication small GTPase-mediated signal transduction Ras protein signal transduction intracellular signal transduction intracellular signaling cassette heart development heart valve development aortic valve development circulatory system development anatomical structure morphogenesis heart valve morphogenesis semi-lunar valve development aortic valve morphogenesis cell morphogenesis involved in neuron differentiation cell morphogenesis negative regulation of apoptotic signaling pathway apoptotic signaling pathway regulation of apoptotic signaling pathway neuron apoptotic process regulation of cell cycle G1/S phase transition negative regulation of mitotic cell cycle negative regulation of cell cycle phase transition negative regulation of G1/S transition of mitotic cell cycle negative regulation of mitotic cell cycle phase transition negative regulation of cell cycle G1/S phase transition negative regulation of cell cycle process regulation of G1/S transition of mitotic cell cycle cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression negative regulation of gene expression, epigenetic anatomical structure homeostasis tissue homeostasis cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus response to hormone response to insulin cellular response to insulin stimulus cellular response to hormone stimulus regulation of myofibroblast differentiation myofibroblast differentiation negative regulation of myofibroblast differentiation negative regulation of cold-induced thermogenesis adaptive thermogenesis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis regulation of lipid kinase activity positive regulation of collagen fibril organization positive regulation of extracellular matrix organization collagen fibril organization extracellular matrix organization regulation of extracellular matrix organization regulation of collagen fibril organization extracellular structure organization external encapsulating structure organization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle SWI/SNF complex ATPase complex protein-containing complex catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle SWI/SNF complex ATPase complex protein-containing complex catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle organelle membraneless organelle SWI/SNF superfamily-type complex cytoskeleton spindle microtubule cytoskeleton chromatin silencing complex chromatin lock complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen RNA polymerase II transcription regulator complex transcription regulator complex Rb-E2F complex nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR024599	Retinoblastoma-associated protein, N-terminal	Domain
A	IPR015030	Retinoblastoma-associated protein, C-terminal	Domain
A	IPR002720	Retinoblastoma-associated protein, A-box	Domain
A	IPR028309	Retinoblastoma protein family	Family
A	IPR002719	Retinoblastoma-associated protein, B-box	Domain
A	IPR036915	Cyclin-like superfamily	Homologous Superfamily
A	IPR013763	Cyclin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P06400	urinary bladder cancer small cell lung carcinoma osteosarcoma retinoblastoma chromosome 13q14 deletion syndrome esophageal squamous cell carcinoma non-small cell lung carcinoma hereditary retinoblastoma adrenal cortex carcinoma skin basal cell carcinoma Stevens-Johnson syndrome gastrointestinal stromal tumor prostate cancer Liver Neoplasms, Experimental Sezary syndrome urinary bladder cancer small cell lung carcinoma osteosarcoma retinoblastoma chromosome 13q14 deletion syndrome esophageal squamous cell carcinoma non-small cell lung carcinoma hereditary retinoblastoma adrenal cortex carcinoma skin basal cell carcinoma Stevens-Johnson syndrome gastrointestinal stromal tumor prostate cancer Liver Neoplasms, Experimental Sezary syndrome brain ischemia breast carcinoma small cell carcinoma sarcomatoid carcinoma bone osteosarcoma breast cancer carcinoma undifferentiated carcinoma childhood acute lymphoblastic leukemia myopathy urinary bladder neoplasm dermatomyositis oligodendroglioma hypotrichosis 8 adrenal gland cancer large cell medulloblastoma rheumatoid arthritis bladder benign neoplasm malignant mesothelioma skin pigmented basal cell carcinoma malignant pancreatic neoplasm mammary neoplasms, animal medulloblastoma cholangiocarcinoma eye disease glioblastoma adrenal carcinoma IgA glomerulonephritis sarcoma astrocytic tumor lung cancer Sjogren syndrome bladder carcinoma in situ breast adenocarcinoma cancer toxic epidermal necrolysis urinary bladder carcinoma hepatocellular carcinoma pancreatic neoplasm primitive neuroectodermal tumor juvenile dermatomyositis atypical teratoid rhabdoid tumor malignant ependymoma

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.