9W7W | pdb_00009w7w

Crystal Structure of NFIB Bound to a Palindromic DNA

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	PF03165	MH1 domain (MH1)	MH1 domain	The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved ...	The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [1,3].	Domain
A, D [auth B]	PF10524	Nuclear factor I protein pre-N-terminus (NfI_DNAbd_pre-N)	Nuclear factor I protein pre-N-terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], F	DNA (5'-D(GAPTPTPGPGPCPAPTPCPTPTPGPCPCPAPAPCP*T)-3')	-	-	-
B [auth C], E	DNA (5'-D(APGPTPTPGPGPCPAPAPGPAPTPGPCPCPAPAPCP*T)-3')	-	-	-
A, D [auth B]	Nuclear factor 1 B-type	molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding	multicellular organismal process regulation of cellular process negative regulation of biological process respiratory tube development epithelial cell proliferation involved in lung morphogenesis multicellular organism development negative regulation of cellular process anatomical structure development lung development respiratory system development lung morphogenesis animal organ morphogenesis epithelial cell proliferation regulation of epithelial cell proliferation involved in lung morphogenesis multicellular organismal process regulation of cellular process negative regulation of biological process respiratory tube development epithelial cell proliferation involved in lung morphogenesis multicellular organism development negative regulation of cellular process anatomical structure development lung development respiratory system development lung morphogenesis animal organ morphogenesis epithelial cell proliferation regulation of epithelial cell proliferation involved in lung morphogenesis system development developmental process negative regulation of cell population proliferation regulation of biological process epithelium development cell population proliferation tube development biological regulation animal organ development lung epithelium development tissue development anatomical structure morphogenesis negative regulation of epithelial cell proliferation involved in lung morphogenesis regulation of cell population proliferation cellular process regulation of epithelial cell proliferation negative regulation of epithelial cell proliferation head development central nervous system development brain development nervous system development hindbrain development regeneration sensory organ development eye development retina development in camera-type eye visual system development camera-type eye development sensory system development regulation of stem cell proliferation negative regulation of stem cell proliferation stem cell proliferation lung ciliated cell differentiation cellular developmental process epithelial cell differentiation multi-ciliated epithelial cell differentiation lung epithelial cell differentiation lung cell differentiation cell differentiation columnar/cuboidal epithelial cell differentiation axonogenesis cell projection organization forebrain development plasma membrane bounded cell projection morphogenesis cell development central nervous system neuron development neuron projection development cell morphogenesis cellular component organization neurogenesis central nervous system neuron differentiation cell projection morphogenesis neuron differentiation neuron projection morphogenesis cellular component organization or biogenesis central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation generation of neurons anterior commissure morphogenesis neuron development telencephalon development maintenance of cell number stem cell population maintenance club cell differentiation cell proliferation in forebrain neural precursor cell proliferation response to stimulus response to stress response to wounding connective tissue development skeletal system development chondrocyte differentiation cartilage development 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 transcription by RNA polymerase II 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process 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 regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process 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 transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process gliogenesis glial cell differentiation salivary gland cavitation gland development salivary gland development tube formation tube morphogenesis gland morphogenesis salivary gland morphogenesis anatomical structure formation involved in morphogenesis tube lumen cavitation exocrine system development DNA replication DNA metabolic process neuron fate commitment cell fate specification neuron fate specification cell fate commitment type I pneumocyte differentiation regulation of developmental process mesenchymal cell proliferation involved in lung development mesenchymal cell proliferation negative regulation of mesenchymal cell proliferation regulation of multicellular organismal process negative regulation of developmental process regulation of mesenchymal cell proliferation negative regulation of mesenchymal cell proliferation involved in lung development negative regulation of multicellular organismal process glial cell fate specification glial cell fate commitment principal sensory nucleus of trigeminal nerve development trigeminal sensory nucleus development neural nucleus development mitotic nuclear division organelle fission cell cycle phase transition exit from mitosis mitotic cell cycle nuclear division organelle organization mitotic cell cycle process cell cycle cell cycle process mitotic cell cycle phase transition commissural neuron axon guidance axon guidance neuron projection guidance cell differentiation involved in salivary gland development negative regulation of miRNA transcription miRNA transcription regulation of miRNA metabolic process miRNA metabolic process negative regulation of miRNA metabolic process regulation of miRNA transcription type II pneumocyte differentiation lung secretory cell differentiation biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis glandular epithelial cell differentiation regulation of molecular function regulation of DNA binding regulation of binding negative regulation of binding negative regulation of molecular function negative regulation of DNA binding glial cell proliferation	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nucleolus fibrillar center axon cell projection neuron projection cerebellar mossy fiber plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR019739	CTF transcription factor/nuclear factor 1, conserved site	Conserved Site
A, D [auth B]	IPR019548	CTF transcription factor/nuclear factor 1, N-terminal	Domain
A, D [auth B]	IPR020604	CTF transcription factor/nuclear factor 1, DNA-binding domain	Domain
A, D [auth B]	IPR003619	MAD homology 1, Dwarfin-type	Domain
A, D [auth B]	IPR000647	CTF transcription factor/nuclear factor 1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D [auth B]	Pharos: O00712	adenoid cystic carcinoma salivary gland adenoid cystic carcinoma malignant mesothelioma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ gastric carcinoma lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm osteosarcoma Pick disease adenoid cystic carcinoma salivary gland adenoid cystic carcinoma malignant mesothelioma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ gastric carcinoma lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm osteosarcoma Pick disease astrocytic tumor bone disease cutaneous lupus erythematosus exocrine pancreatic carcinoma invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma ovarian cancer pituitary cancer transitional cell carcinoma attention deficit hyperactivity disorder, inattentive type breast cancer dermatomyositis gastric cancer large cell medulloblastoma lung carcinoma

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.