7MI8

Signal subtracted reconstruction of AAA5 and AAA6 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Model 5

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18198	Dynein heavy chain AAA lid domain (AAA_lid_11)	Dynein heavy chain AAA lid domain	This family represents the AAA lid domain found neat the C-terminal region of dynein heavy chain.	Domain
A	PF12774	Hydrolytic ATP binding site of dynein motor region (AAA_6)	Hydrolytic ATP binding site of dynein motor region	This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydro ...	This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities: AAA1-AAA6) [1]. This is the first site (out of four nucleotide binding sites in the dynein motor) where the movement depends on ATP hydrolysis [2]. When this site is nucleotide free or bound to ADP, the microtubule binding domain (MTBD) binds to the microtubule and the linker adopts the straight post-power-stroke conformation. Upon ATP binding and hydrolysis, the MTBD detaches from the microtubule and the linker is primed into the pre-power-stroke conformation. Dynein's AAA+ domains are each divided into an alpha/beta large subdomain designated with an L and and alpha small subdomains designated with an S. This is the AAA1 large (AAA1L) subdomain with the accompanying small subdomain (AAA1S). AAA1L, AAA1S and AAA2L enclose ADP.vanadate (ADP.Vi, ATP-hydrolysis transition state analogue). The AAA1L sensor-I loop, which varies in position depending on dynein's nucleotide state, swings in to contact AAA2L forming the important AAA1 nucleotide-binding site [1].	Domain
A	PF03028	Dynein heavy chain region D6 P-loop domain (Dynein_heavy)	Dynein heavy chain region D6 P-loop domain	This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved i ...	This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains [1]. The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This C-terminal domain carries the D6 region of the dynein motor where the P-loop has been lost in evolution but the general structure of a potential ATP binding site appears to be retained [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Fusion protein of Dynein and Endolysin	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 dynein light intermediate chain binding protein binding microtubule motor activity cytoskeletal motor activity minus-end-directed microtubule motor 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 dynein intermediate chain binding hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity	establishment of organelle localization cellular localization organelle transport along microtubule transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration along microtubule microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport establishment of organelle localization cellular localization organelle transport along microtubule transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration along microtubule microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement microtubule-based process nuclear migration organelle fusion cellular component organization organelle organization nucleus organization karyogamy cellular component organization or biogenesis microtubule cytoskeleton organization spindle localization mitotic cell cycle establishment of mitotic spindle localization mitotic cell cycle process establishment of spindle localization cell cycle microtubule cytoskeleton organization involved in mitosis cytoskeleton organization cell cycle process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation nuclear division mitotic sister chromatid segregation nuclear chromosome segregation chromosome segregation cytoplasmic microtubule organization supramolecular fiber organization establishment or maintenance of cell polarity establishment of spindle orientation establishment of cell polarity establishment of mitotic spindle orientation mitotic spindle organization spindle organization biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process macromolecule metabolic process symbiont-mediated cytolysis of host cell viral life cycle disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction viral release from host cell by cytolysis disruption of cellular anatomical structure in another organism exit from host cell viral process cytolysis in another organism viral release from host cell disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing disruption of plasma membrane integrity in another organism cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process	cell periphery cell cortex cellular anatomical structure intracellular anatomical structure cytoplasm polymeric cytoskeletal fiber spindle aster astral microtubule intracellular membraneless organelle spindle microtubule cytoplasmic microtubule intracellular organelle cytoskeleton cell periphery cell cortex cellular anatomical structure intracellular anatomical structure cytoplasm polymeric cytoskeletal fiber spindle aster astral microtubule intracellular membraneless organelle spindle microtubule cytoplasmic microtubule intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton microtubule organizing center spindle pole body protein-containing complex cytoplasmic dynein complex catalytic complex dynein complex microtubule associated complex host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR026983	Dynein heavy chain	Family
A	IPR013602	Dynein heavy chain, linker	Domain
A	IPR035706	Dynein heavy chain, ATP-binding dynein motor region	Domain
A	IPR054354	Dynein 2 heavy chain 1, cytoplasmic, ATPase lid domain	Domain
A	IPR003593	AAA+ ATPase domain	Domain
A	IPR041658	Dynein heavy chain AAA lid domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR042228	Dynein heavy chain, linker, subdomain 3	Homologous Superfamily
A	IPR035699	Dynein heavy chain, hydrolytic ATP-binding dynein motor region	Domain
A	IPR042219	Dynein heavy chain AAA lid domain superfamily	Homologous Superfamily
A	IPR024743	Dynein heavy chain, coiled coil stalk	Domain
A	IPR013594	Dynein heavy chain, tail	Domain
A	IPR048404	DYN1, AAA+ ATPase lid domain	Domain
A	IPR043157	Dynein heavy chain, AAA1 domain, small subdomain	Homologous Superfamily
A	IPR042222	Dynein heavy chain, domain 2, N-terminal	Homologous Superfamily
A	IPR004273	Dynein heavy chain region D6 P-loop domain	Domain
A	IPR024317	Dynein heavy chain, AAA module D4	Domain
A	IPR052619	Bacteriophage lysozyme-like	Family
A	IPR001165	T4-type lysozyme	Family
A	IPR034690	Endolysin T4 type	Family
A	IPR002196	Glycoside hydrolase, family 24	Family
A	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily

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.

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7MI8

Signal subtracted reconstruction of AAA5 and AAA6 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Model 5

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage