4NOD

Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation

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)
A	PF00505	e4nodA1	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: PF00505	ECOD (1.6)
A	PF09011	e4nodA2	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: PF09011	ECOD (1.6)
B	PF00505	e4nodB1	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: PF00505	ECOD (1.6)
B	PF09011	e4nodB2	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: PF09011	ECOD (1.6)
G	PF00505	e4nodG1	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: PF00505	ECOD (1.6)
G	PF09011	e4nodG2	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: PF09011	ECOD (1.6)
H	PF00505	e4nodH1	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: PF00505	ECOD (1.6)
H	PF09011	e4nodH2	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: PF09011	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)
B	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)
G	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)
H	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, G, H	PF00505	HMG (high mobility group) box (HMG_box)	HMG (high mobility group) box	-	Domain
A, B, G, H	PF09011	HMG-box domain (HMG_box_2)	HMG-box domain	This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long ...	This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, G, H	Transcription factor A, mitochondrial	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding transcription coactivator binding mitochondrial promoter sequence-specific DNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding transcription coactivator binding mitochondrial promoter sequence-specific DNA binding protein-containing complex binding chromatin binding heat shock protein binding RNA binding transcription regulator activity mitochondrial transcription factor activity	cellular biosynthetic process RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process transcription initiation at mitochondrial promoter cellular metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process cellular biosynthetic process RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process transcription initiation at mitochondrial promoter cellular metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process mitochondrial RNA metabolic process response to decreased oxygen levels response to stimulus response to hypoxia response to stress response to oxygen levels response to abiotic stimulus regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary 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 regulation of biological process positive regulation of nucleobase-containing compound metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cellular component organization cellular component biogenesis organelle organization cellular component assembly mitochondrial respiratory chain complex assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis mitochondrion organization response to nutrient levels response to chemical response to nutrient	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle mitochondrial nucleoid non-membrane-bounded organelle protein-containing complex nucleus
C, D [auth E], I, J [auth K]	5'-D(TPTPGPGPGPGPTPAPTPGPGPGPGPCPTPTPGPGP(BRU)PTPGPG)-3'	-	-	-
E [auth D], F, K [auth J], L	5'-D(CPCPAPAPCPCPAPAPGPCPCPCPCPAPTPAPCPCPCPCPAPA)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, G, H	IPR009071	High mobility group box domain	Domain
A, B, G, H	IPR036910	High mobility group box domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, G, H	Pharos: Q00059	Alzheimer disease mitochondrial DNA depletion syndrome 15 (hepatocerebral type); secondary Parkinson disease Bowen disease of the skin Ceroid lipofuscinosis, neuronal 1, infantile plasma cell myeloma malignant mesothelioma nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous neoplasm large cell medulloblastoma medulloblastoma osteosarcoma rheumatoid arthritis lung cancer ovarian cancer

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 R01GM133198.