4NOD | pdb_00004nod

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	PepSY_like	e4nodA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
H	PepSY_like	e4nodH1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
G	PepSY_like	e4nodG1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
B	PepSY_like	e4nodB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)

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)
H	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)
B	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	transcription factor binding transcription coregulator binding protein binding binding transcription coactivator 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 transcription regulatory region nucleic acid binding mitochondrial promoter sequence-specific DNA binding chromatin binding transcription factor binding transcription coregulator binding protein binding binding transcription coactivator 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 transcription regulatory region nucleic acid binding mitochondrial promoter sequence-specific DNA binding chromatin binding heat shock protein binding RNA binding transcription regulator activity mitochondrial transcription factor activity	RNA metabolic process primary metabolic process mitochondrial gene expression gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process RNA metabolic process primary metabolic process mitochondrial gene expression gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription initiation at mitochondrial promoter 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 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membraneless organelle mitochondrial nucleoid 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	IPR050342	High Mobility Group Box (HMGB)	Family
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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.