7UPR | pdb_00007upr

Human mitochondrial AAA protein ATAD1 (with a catalytic dead mutation) in complex with a peptide substrate (closed conformation)

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
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth C]	Vps4_C_C	e7uprC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
A [auth C]	Sigma54_activat	e7uprC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
B	Vps4_C_C	e7uprB2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
B	Sigma54_activat	e7uprB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
C [auth E]	Vps4_C_C	e7uprE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
C [auth E]	Sigma54_activat	e7uprE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
D	Vps4_C_C	e7uprD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
D	Sigma54_activat	e7uprD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
E [auth F]	Vps4_C_C	e7uprF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
E [auth F]	Sigma54_activat	e7uprF2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
F [auth A]	Vps4_C_C	e7uprA2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
F [auth A]	Sigma54_activat	e7uprA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
C [auth E]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	PF17862	AAA+ lid domain (AAA_lid_3)	AAA+ lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G	Unknown peptide substrate	-	-	-
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	Outer mitochondrial transmembrane helix translocase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding membrane protein dislocase activity protein transporter activity transporter activity ATP-dependent activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	localization establishment of protein localization cellular localization establishment of protein localization to membrane cellular process localization within membrane extraction of mislocalized protein from membrane establishment of localization extraction of mislocalized protein from mitochondrial outer membrane behavior multicellular organismal process system process learning learning or memory localization establishment of protein localization cellular localization establishment of protein localization to membrane cellular process localization within membrane extraction of mislocalized protein from membrane establishment of localization extraction of mislocalized protein from mitochondrial outer membrane behavior multicellular organismal process system process learning learning or memory nervous system process cognition regulation of cellular process negative regulation of signaling signaling modulation of chemical synaptic transmission synaptic transmission, glutamatergic negative regulation of biological process regulation of synaptic transmission, glutamatergic negative regulation of synaptic transmission negative regulation of cell communication cell communication synaptic signaling negative regulation of cellular process trans-synaptic signaling regulation of signaling regulation of biological process biological regulation cell-cell signaling chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication negative regulation of synaptic transmission, glutamatergic regulation of localization import into cell regulation of cellular component organization positive regulation of cellular component organization receptor internalization transport positive regulation of biological process regulation of receptor internalization vesicle-mediated transport cellular component organization positive regulation of endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport positive regulation of receptor internalization positive regulation of transport endocytosis receptor-mediated endocytosis memory postsynaptic neurotransmitter receptor internalization vesicle-mediated transport in synapse establishment of localization in cell regulation of postsynaptic neurotransmitter receptor internalization regulation of biological quality neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery postsynapse postsynaptic membrane synapse cell junction membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane cytosol mitochondrial membrane organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane peroxisome microbody membrane peroxisomal membrane microbody glutamatergic synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	IPR051701	Mitochondrial Outer Membrane Translocase MSP1 Subfamily	Family
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	IPR003593	AAA+ ATPase domain	Domain
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	IPR003959	ATPase, AAA-type, core	Domain
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C], B, C [auth E], D, E [auth F], A [auth C], B, C [auth E], D, E [auth F], F [auth A]	Pharos: Q8NBU5	atypical teratoid rhabdoid tumor hyperekplexia 4 malignant glioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm colorectal cancer large cell medulloblastoma medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia glioblastoma malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth C], B, C [auth E], D, E [auth F] A [auth C], B, C [auth E], D, E [auth F], F [auth A]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	AAA-ATPAse Membrane Translocators	AAA protein ATAD1 (with a catalytic dead mutation) in complex with a peptide substrate, closed conformation

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.